They're attacking people and wrecking the place. Clearly they need to be stopped. Sure, it would be a bad idea for her to go all super sayan on them like she did with Tirek, but we've seen her use magic to restrain ponies without hurting them:

She could totally pull the same trick on these guys and end the story in about five minutes . . . which I guess is why she doesn't. (But then why not just frame the story so that she isn't there?)

Um… what? Yeeeaaaaaahhh… this really isn't the kind of moral stance Twilight's character is able to take… nice try with that though.

Hell, just the villains alone… Nightmare Moon, Discord, Sunset, the sirens, she was totally going to attempt to use her shit on Chrysalis. There can be some debate if Sombra was actually "living" at the time he was killed. And I'm not sure if Tirek can count as someone who "thinks" as he's pretty braindead…

Hell, this is the same person who was more than willing to alter the habits of entire species to suit her needs.

I suppose it's there way of working around the "Well, if Twilight uses her magic, there'd be no plot," nonsense. But that's when you realize you should probably change something here and there, in order to make that not a problem…