Really? He destroyed them because they were his enemies? How is that remotely deducible from that episode? He did that to extort information from them, not because he was embroiled in good vs. evil battle against their forces as in times past. He destroyed them to prove a point - which is spelled out in dialogue on Demon's Run itself a few scenes later. That's entire point of the scene. Did you miss that? The Doctor embraces overkill now. He's not engaging in actions for the sake of the greater good in that story; he begins showing off. He does things because he can, not because he must; he's allowing vengeance to rule him, not ruling his vengeance.
The point of the episode is that the Doctor has reached a tipping point. He's become reckless. He's become arrogant. He's not just confident; he's overconfident, and he'll now ride roughshod over you if you get in his way. He's forgotten that "Doctor" means "healer" and a person to be welcomed and admired, and not stopped to consider that his name has come to mean "Great Warrior," in some quarters, and feared and dredded by good and bad alike. His actions have reached a point in which they terrify otherwise good people. His enemies aren't acting out because they are Nazi's bent on destruction of all that is alien, like the Daleks, or to improve others and survive (Cybermen) or take over the universe (the Master) or overcome space and time (The Time Lords). They are simply afraid of him. That's it. They are, like the alliance in Season 5, trying to preserve the universe from what they fear the Doctor has become or may become in the relative future. That's a meme that Moffat has gone waaaay out of his way to repeat not just this year, but last year as well. You can call that BS and deny it all you want - but it's what the show has explicitly stated and demonstrated.
