Pepper didn't mind the under the shirt touching as long as it was gong to remain chaste. As much as she wanted to, she didn't want to sleep with Tony and break him in bed or something. Her worst worry was having to explain to Dr. McTaggert that the reason he was back in the ER was because they couldn't wait to have sex.
Once they were inside though Pepper lead Tony to the couch and sat down so she could resume that whole making out thing. Yeah, she wanted more of that.