I felt given he protested vigorously and thought about how he didn't want to enjoy it and cried during, it was pretty clear. I mean, he denied consent as best he could given he was gagged.

I can kind of see Tony (after the rape happen) accepting what happened and admitting to himself that he wanted it

Given Tony's issues, yes, I can see that, but that would be a comforting delusion on his part. He would very possibly convince himself Steve hadn't really raped him. He would be wrong.