You're right that we have to judge each issue as it's released, but we also have to judge them within the context of being part of a serial. It certainly *is* an upsetting possibility that a character may have been raped, but personally, I don't remember reading many "I am upset that Michelle may have been raped" comments. I do remember, on the other hand, borderline libelous attacks against Marvel freelancers and editorial staff by readers who were assuming the misdirection to be fact. Some posts even pointed out that intercourse wasn't certain based on the text, and they were belittled for it!
As for the "humorous light" part: I sort of think it *is* to soon to be upset by that, but, I definitely see that as subjective. 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. Michelle doesn't know anything is wrong at all. So, there hasn't been time for drama to kick in yet.
Plus... mistaken-identity romantic hijinx are a pretty well-established storytelling trope. Briefly playing it in that direction, while the characters still don't know the score, doesn't seem out of line to me. Given that practically every Shakespearean comedy relies on it, and there's not a lot of outrage about those as far as I know, I'm not surprised that Van Lente seemingly didn't expect this sort of reaction from readers.