But no, apparently she thinks that Tony wronged her and was a dick, as well!

Uh... she did have to undergo major surgery to bring Tony back, which he just kind of assumed she'd do. I can see her being annoyed she wasn't let in on the plan, especially if she slept with him on the grounds it would be the last time they ever saw each other.

(Also, sexual consent of brain damaged people is a really, really tricky scenario. They're often still people with desires and agency; and in a situation where Tony isn't going to recover and will die shortly,(as Pepper believed) that's rather less skeevy.)