Both he and Prentiss find ways to voice their dislike of Strauss in a professional setting. Prentiss' "Ma'am" is one of my top 20 moments on the show.

In this instance, though, I think Morgan was just operating under the impression that she was his partner and they were in the field on a case, so he was reacting to her the way he would anyone else on the team. She was going a bit off the rails, he was thinking he smelled alcohol, and he was trying to get her attention and reign her in.