When the "sliding to the floor" panels were first posted I remember a lot of comments like "ew" and "whoa whoa whoas...isn't that rape?" Later the comments shifted from displeasure that the perceived rape was being played with a light, inappropriate tone.
My view is that Peter just found out at the end of the last issue that something -- he doesn't even know what -- happened while Chameleon was there.
I think Peter should be much more alarmed in the panels where we do see his reaction because he doesn't know what happened. It kicks in enough for Peter to think "Chameleon, when I find you, I will kill you." But it's not in reaction to the fact that the Chameleon, who Peter knows is a murderer and could have done all kinds of creepy, terrible stuff to Michelle when he was alone with her, may have raped his roommate while wearing his face, it's in reaction to the fact that he is now expected to snuggle a woman he doesn't like.
It's a common trope, yes, but I think "Dangerous supervillain breaks into a woman's home in disguise and makes sexual advances on her" should not be used as the basis for romantic hijinx. To me, it's much too serious for that. As for Shakespeare, I don't think many people read plays written in the 16th century and expect them to be particularly enlightened regarding gender and sexual politics--there's a lot of contemporary criticism about whether the love potion in Midsummer Night's Dream takes away consent and identity, for example.