I actually ran into Scott Adsit in the city a few weeks ago (which was **QWOP** awesome.) I wasn't going to post anything because I didn't want him to get in trouble for telling me anything, but since it seems like it's rumored, I'll talk. He told me that yes they are working on a season 2 of Frankenhole, and that they had to promise Adult Swim that they wouldn't give it any Moral Orel-esque twist like the hunting trip episode.
I've been kicking myself for not asking him about the Mother Theresa episode since, I knew I should have prepared a list of questions for the day I might accidentally run into Scott Adsit on the street. But either way, he told me that yes there is a new season coming. (Of course, he might have just said that to get the drooling fanboy away from him.)