If you consider murdering one's siblings to be abuse then yeah. And that possibility is always there but with the death of her brothers she was technically next in line to the throne and it made sense to closely supervise anyone in your custody who technically had a greater claim than you did. A woman had never taken over the throne regardless of being the rightful heir at this point, but that didn't bode true for the children/descendants of said women, and Elizabeth was thus a threat to his rule. Maybe not one he would murder given the sensibilities of the age, but one he wasn't going to let escape or anything. Cause according to history if she had a kid, the kid or one of the kid's descendants were going to take power at some point(I mean this is how the House of York gained power in the first place, the rightful heir was a woman no one recognized her claim until a male descendant who was willing to fight for it came along). And of course Elizabeth was the means through which Henry VII's children became the rightful heirs to the throne regardless of Elizabeth not being Queen which based on pure hereditary succession she should have been in a non Salic system. Since her children would succeed Henry that distinction became irrelevant.