I think that is why Moftiss did underline the fact that Sherlock had committed murder, and had his brother, whom we know loves him deeply, pronounce that verdict.

Had they attempted to use the Mary gambit they would have come unstuck; even if heroes don't exist they still have to play by the rules of the game, and those rules never include murder for personal gain. Indeed, in the end we have the stark contrast between Sherlock, who accepts that he must pay the price for his actions, and Mary, who sees nothing wrong in killing a subset of people she defines as being less than human, and therefore are not entitled to the human right to exist.

I expect Moftiss to explore this further in the next season because it really does need to be explored...