[John sits up a little straighter, his expression a bit more serious. His personality may be out-of-synch with the age and experiences of his current body, but for a moment, he looks the part.]

You're really insistent the two memories you have of being two types of Sherlock are pretty close to identical, when you get down to it. That even if there are some changes, you're basically the same person.

Then that means that even if I don't have his memories, I'm an awful lot like the John whose body I'm in. I know I wouldn't kill someone unless I had a reason so good that I wouldn't regret it for a second, so he must've had one when he killed someone for you.

And if he's stuck around and lived with you for a year even with all the body parts, then there must be some good in it.