WTF; What Da Fuq?!?! this is making Martin out to be one of the most inconsistent, flip flopping, characters i've ever seen, and it's coming from out of nowhere.
Inconsistency has a consistency all its own. How many times have you heard someone say something like, "I just don't understand (insert gender)!" It usually boils down to an unwillingness or inability to look at things from a different view point.
Marten's behavior makes perfect sense if you accept the possibility that he was simply unaware of direction his feelings were going. He had previously declared that he wasn't going to be banging "his" interns. Yet, from the beginning, he was interested in Claire. It probably wasn't romantic at the start, but she was someone he tended to seek out.
That's called internal conflict. That's how stories get told. The Emily arc serves to put that conflict front and center. Ultimately, Marten is not freaking out because his "intern banging" rule is at risk. He probably freaked because he is too nice--therefore worried he'll hurt Emily's feelings--and because it seems like the wrong intern is interested in him.
HiFranc has it right to suggest Marten may have been in denial right up until he actually had a chance to talk to Claire. Jeph doesn't show us his characters' thoughts often, and leading up to the critical moment, we saw a lot less about what Marten was thinking than usual--mostly because Marty didn't talk to anyone about it.
But we do know that he didn't handle it in an un-Marten like manner. He thought things over to the point that he had a big speech planned. That's totally Marten.
The important point is that Marten's actions only seem like a flip if you assume that he was serious about not dating an intern. I expect Faye is going to be making that point, especially given her concern about Tai finding out. Now that she knows Tai is okay with it, it fair game to razz Marten for overreacting about Emily.