Hmmm, I may have to try and watch that again, because I did get that impression. From what I remember they were a bit uncomfortable and awkward with each other, at least until the very end of the episode when they make a peace of sorts.
Then the comment Prentiss made to Hotch in another episode about how much she hated politics and how it destroys families. Struck me as being very much spoken from experience.

And now am very curious and may just have to watch some CM this weekend. *g*