Khokhars are not Rajputs, no source prior to the British calling them Rajput. Even Janjuas are of doubtful stock considering its a Jatt surname.Sorry i was not paying attention. I dont know much about Muslim Rajputs. The only Muslim Rajputs that i am familiar with, are Khokhars, Janjuas, and Bhattis of Punjab, and Mewatis.
I have not come across any source which says that Rajputs were backbone of the armies of Delhi sultanates (Ilbari, Khalji, Tughlaq, Sayyid and Lodi). From Tarikh-i-Feroz Shahi it appears most of the Indians serving in the nobility and army belonged to menial castes, so most of them could not be Rajputs. It appears Hindus were of heterogeneous background and no particular region was given special preference. Afghans were also not the backbone of the sultanate armies up to 1400 AD. According to Al Umri (1300-1349), the army of Muhammad Tughlaq consisted of Turks, inhabitants of Khata, Persians, and Indians. The rise of Afghans is linked with Sayyid dynasty (according to Khafi Khan, ancestors of Khizr Khan were Afghans......perhaps he was a fake Sayyid).
The Sultans of Delhi simply did not need Rajputs to lean on as Afghans were not in the picture. Afghans had settled in large numbers in northern India and some local power with equal martial spirit were needed by Mughals to counteract Afghans. After fall of Lodi dynasty, numerous Afghans in northern were nuisance so Babur tried to incorporate them in his nobility, he did not pay attention to Rajputs. His son Humayun got beaten by Afghans and in Persia, as mentioned before, he developed the thought that Afghans had to be counteracted with a regional martial nation of India. Akbar followed the policy of his father. Jahangir relaxed the policy of his father and some Afghans attained high positions in the Mughal nobility and army. But they were never appointed governors (with exception of Khan Jahan Lodi) and were never appointed supreme commander of any army.