idunno, something about the doctor made me think early on that hannibal was gonna kill him anyway. i can't quite put my finger on it. hannibal's definition of "rude " can go a long way. franklin simply unnoticingly placing a used napkin on the table in a very emotional state even bothered him. and plus he could've also either been wanting to make will believe that he himself killed the doctor, or making sure the doctor doesn't tell will about his condition.
but yea, watching him killing the doctor was indeed very creepy. the raincoat, the calmness of the action , like " oh, don't mind me, i'm just cutting someone's ****ing face open , no big deal " , his face as he caught georgia's scent realizing she was there, everything just SCREAMED hannibal lecter in an extremely creepy way.