No, it actually makes sense. Because Sherlock and Moriarty could actually be good friends if Jim wasn't such a dick to him all the time. Now, I don't think that John would ever be able to look past his sociopathic-ness but he'd be reluctantly willing to tolerate him because Sherlock is his bestie and he's already used to his shit at this point so he might as well be supportive (doesn't mean he won't kill Moriarty if he did something to him). So, it does make sense, in an essence.
