Pepper wasn't exactly thinking about any of the bad things anymore. She was starting to remember why she loved this man and all of the good things about him. Maybe it was finally time for her to make her own little confession, but during sex was probably the worst possible time for her to blurt out I thought I was pregnant, but I'm not so it's okay now. It could wait for later.
All of those thoughts just melted away as Tony pushed himself inside of her. All she could think about was just how much she wanted him and how happy she was that they would spend the rest of their lives together.