The building of the Tokugawa State was not as violent,
That is because by the time Tokugawa Ieyasu took power there were no powerful clans and Japan had already been governed as a state and unified by Hideyoshi for 10 years across all of Japan. The way that Hideyoshi organized Japan was that he kept many of the major clans in Japan at the time, barring Hojo Ujimasa and Oda Ujiharu, allowing each clan to have at least one province roughly. There was no scenario in which Tokugawa Ieyasu was going to conquer every province, and uproot every daimyo. Additionally the many daimyo took sides and since approximately half the country supported Toyotomi Hideyori, much of the eastern half supported Tokugawa Ieyasu. It was a conflict that didn't even last a year.
and in the same scale of violence, as what Nobunga was trying to build. A para-feudal hierarchy - that was the hallmark of the Tokugawa's power relations - implies a high level of conciliation that for me would be unacceptable for Nobunaga to accept.
Yeah but Nobunaga was campaigning since 1551 until 1582. It was 1568 when Nobunaga took Kyoto and that is more or less when the "war of unification" had begun. Although Nobunaga likely did not originally intend it as such, he probably only had regional designs on the Kinai Region, completely ignoring everything to his east. But one thing led to another and the war expanded into the Hokuriku Region, the Chugoku Region, and Koshinetsu Region, and these were largely defensive conflicts as Nobunaga had good relations with Uesugi Kenshin, Takeda Shingen, and Mori Motonari. He did not break his alliances and begin the wars in all three cases.
For Hideyoshi and Tokugawa Ieyasu they already could take advantage of a unified state, for Hideyoshi at least in a part of the country. He also gradually won the support from many of Nobunaga's generals. It was only later that he vassalized important clans like Mori, Chosokabe, Shimazu, Otomo, Uesugi, and the many smaller clans of the Kanto and Tohoku regions. Hideyoshi wiped out the Hojo of his own accord.
But that being said Nobunaga had already wiped out all of the major clans in the Kinai Region (the Ashikaga Shogun, the Miyoshi, the Azai, the Asakura, the Sasaki), in addition to the Takeda clan in the Koshinetsu Region and the Imagawa in the Tokai Region. As well as the Ikko Ikki Buddhist zealots, who although not a clan and never had any legitimacy they nonetheless controlled fortresses in many provinces. The Mori and the Uesugi had also suffered many defeats and would have been defeated in due time. Without any of these things then Hideyoshi would not have been able to unify the country, and therefore neither would Tokugawa Ieyasu, who merely usurped Hideyoshi's regime and used it as a basis for his own government.
Nobunaga who was a minor warlord in Owari could not have conciliated other barons in Owari, much less major clans like Imagawa and Takeda. Even when he was on good terms with clans like Mori, Takeda, Uesugi, and Azai, they still changed sides and made war against him. Nobunaga had received the submission of the Hojo Clan around 1578, but when Nobunaga died in 1582 the Hojo immediately made war on the Oda and the Tokugawa. When Nobunaga became lord in 1551 he immediately had to face rebellions from barons in Owari as well as rebellions from his own family. That was just the nature of the feudal power dynamics in the Sengoku Jidai.
Mount Hiei was a controversial incident precisely because Nobunaga himself was a controversial bloody character. Not only that, Oda relentlessly burned down the entire northern district of Kyoto and gave permission to their soldiers to kill indiscriminately its civilian residents, when he faced Ashikaga Yoshiaki's plot against him.
Nobunaga had not cemented his reputation as a ruthless character. It was the destruction of Mount Hiei in 1571 that created this reputation and led to various warlords decrying his ruthlessness publicly. But probably all of these warlords were using it for their own political ends. Especially Takeda Shingen who was not any less ruthless than Oda Nobunaga was. Nobunaga also brutally suppressed the Ikko Ikki in various provinces such as Ise, Omi, Echizen, Settsu, Izumi, Kii, and Kaga.
But the brutal eradication of the Ikko Ikki was not controversial at all, again with the exception of political maneuvering. As all warlords and governors had been required to fend off the Ikko Ikki in years past and utilized equally brutal methods. For example the Miyoshi in Settsu and Izumi, Tokugawa Ieyasu in Mikawa, and Uesugi Kenshin in Etchu Province. The only one who had a problem with this was again the unscrupulous Takeda Shingen who had an existing alliance with the Ikko Ikki abbot, who was married to Takeda Shingen's sister. But the general perception of the Ikko Ikki was that they were a dangerous cult that had quite literally been chased out of multiple towns and provinces, and were a challenge to the mainstream accepted religious organizations.
Other mainstream temples were generally regarded with reverence, however many of them were militant institutions that did not answer to the state. So Nobunaga began a policy of bringing warrior monks to heel using military force, and confiscating or else taxing those temples that decided to be compliant. That is really what made the Mount Hiei incident so controversial. Since Mount Hiei was home to the monks of the Enryakuji, a temple order that was venerated and had a special place in Japanese society for hundreds of years. However the temple complex housed an order of warrior monks that had in centuries past raided Omi and Kyoto and exacted tribute from the surrounding area. When Mount Hiei gave aid to the Asakura and Azai and rejected Nobunaga's demands he considered them an enemy.
It was not so much that a slaughter was carried out, that was common place in Sengoku Era Japan. But the controversy was more so who was being slaughtered and where. The populace and the state at large venerated Mount Hiei and its monks, it wasn't necessarily justified that they were treated with such reverence, but the fact that Nobunaga went with an army to annihilate a religious order and destroy one of the most sacred temples in all of Japan was the actual problem. This event created his reputation as a brutal warlord. This was prior to the suppression of militant temples, prior to the war with the Ikko Ikki, and prior to the destruction of any major clans. Up to this point Nobunaga had not carried out any notable large scale destruction, nor instigated too many wars against rival clans. His only war at this time was against Asakura and Azai, and the remnants of the Sasaki which had been defeated in 1568 when Nobunaga took Kyoto. The Miyoshi which had been defeated in 1568 were neutral at this point.
Attacking a district in Kyoto later on in 1573 was unrelated. But in any case it was tied to the overthrow of the Ashikaga Shogunate. The deliberate action did have its intended effect and Kyoto surrendered. It became associated as punishment for the actions of Ashikaga Yoshiaki. Then Nobunaga took the reins of government and began to be seen as more legitimate than Yoshiaki. Generally in Japan that kind of slaughter and destruction was to force an enemy into submission and often times it did work. Since Japan had a very hierarchical society it was not necessarily viewed as an unjust action if indeed it could be justified, and if it succeeded. Ashikaga Yoshiaki turned against Nobunaga, thereby causing Kyoto itself to become complicit, then Yoshiaki was defeated by Nobunaga which naturally is a sign that he was not the rightful ruler, to add insult to injury he was then banished and the Ashikaga regime was toppled, only for the perpetrator of the attack to take power and form their own government. That is a just action and Nobunaga's regime became sanctioned by the Emperor, and therefore by Heaven.
Then Nobunaga continued to have success in the field, in fact in 1573 alone he defeated the Shogun, the Azai, the Asakura, and the Miyoshi. Clearly this was a ruler that was sanctioned by Heaven, and the rebellion of the Shogun and Kyoto at large had been adequately and proportionally punished. Kyoto was allowed to submit to Nobunaga, who acted in the Emperor's name against the corrupt and inept Shogun, who in any case was an enemy of the Emperor through his misdeeds and his neglect of his Imperial duties. Much like Hideyoshi who although was a dirty peasant was able to unify Japan, get sanctioned by the Emperor, and then when he died the Emperor declared that he was a deity. The tyrannical rule of Hideyoshi and all of the executions and brutal policies are therefore brushed under the carpet.
Any brutality that was against a criminal, a rebel, or a defeated enemy fighting against a more legitimate power was more or less justified. Which is why Kyoto was allowed to surrender in 1573, or the Ikko Ikki were allowed to surrender in 1580, or Sakai was permitted to surrender in 1570 and Nobunaga used similar strong arm tactics as he did in Kyoto against that latter city. So the level of destruction perpetrated by a daimyo was usually relative to their level of success. For example if Takeda Shingen or Hojo Ujimasa had conquered as many provinces as Nobunaga had, then they would have destroyed as much as Nobunaga did.
The only reason that Hideyoshi and Tokugawa Ieyasu were able to get away with their "conciliation" is because the country had already been largely unified and they could make use of a pre-existing government. But even Tokugawa Ieyasu had attacked and sacked the city of Sakai. Use of violence against acceptable targets was not controversial at all in Japan. There did not exist a "just war" concept like the one defined by Thomas Aquinas. While rule of law was practically non-existent, the daimyo and their armies decided what was legal, and the peasants as well as anyone under the daimyo was required to accept it as such. There may have been resentment but that did not make their regime illegitimate. Even temples were not off limits although those were more controversial targets. But attacking temples was so common that many of them were fortified and utilized by lords as fortresses against their enemies. Again, with Mount Hiei the controversy was more because of its almost unique status as one of the most holy temples in Japan, that housed one of the most sacred orders in Japan.