He's finished his internship (what a horrible word) although he'll have an excuse to hang around as Masuka said he'll send him some work from time to time. I don't see how they can make him a baddy yet although he may spend most of the next series trying to get Dexter's attention in one way or another like with the hand.
A lot depends on the Big Bad, really. A good villain goes a long way. I just hope it isn't the intern. Although it would be pretty interesting to have the Big Bad working for the police.