Since you already received an email from her, I think if you won't be too stressed out by it, it would be good to just stick with that. The fact that she's so happy to be included does bode well for a friendship if you want one. I would of course make sure that in the future I say I have to think about things if I'm conflicted about the answer. Of course if it would make you miserable, you should not feel forced to go through with it.
What I'd want to do is discuss with him "I was surprised you are so affectionate with me in general but were not when your girlfriend was around, it made me feel a bit uncomfortable" and then discuss that with him. That way he can tell you the reasoning, if it was a one time only thing to make sure that both of you got along or whatever, and you can figure out if it is going to be his behavior in the future, what to expect on Thanksgiving, and so on.
Hey that's tomorrow, hope if everybody shows up you have a fabulous time!
Happiness will never come to those who fail to appreciate what they already have.