If you think that Boffinspark's little tantrum after being disavowed was him going evil, than your even more naive than I thought. Given the arsenal at his command, if the nutcase had really wanted to he could have done a lot more than knock a few holes in Canterlot (in case you've forgotten, Dive Bomb was the one who actually blew up Canterlot). Frankly, I'd be willing to bet that the only reason the professor even fired on Canterlot in the first place was he bother to check the coordinates of Silent Night's little tea party.
And to be honest, I'm not entirely sure I could stop him if he really went off the deep end. Granted, I might be able to take him down, but there's an even chance he'd just portal me out of the ship and use me as target practice. In the end, it's safer to let him remain Celestia's loyal little psychopath.