The interviews with Lithgow said that he was the one that killed Rita, so it was difinitely Trinity. If you go back and watch the kill scene, he's kind of telling Dexter that he can't have it all, and he's been one-upped, even though he knows he's about to die. He's at peace with it.
I'm so happy they killed of Rita. I really hated her character. The way they did it really did give the heart strings a tug, but overall, I'm pleased. I think this will open a lot of doors that were closed for Dexter this season.
And if anyone has read the books...the sequels set up Aster and Cody to start following in Dexter's footsteps, where he starts to share his code with them. Not sure if the show will take that direction, but it seems to make sense, particularly with Harrison sitting in Rita's blood, etc...
I'm so excited to see where they head with next season! There's really nothing that they CAN'T do at this point!!!