Police aren't the bad guys simply because they put people in jail; it's because those people are twisted, demented. Sure, they have done mistakes but at the end of the day they had to do what they had to do. Celestia is no different:
"Dangerous", but important missions. She sent them for a reason, she ain't keeping them around just to make them feel happy and all that.
Sending her own sister to the moon which was just absolutely twisted in KILLING Celestia, not to mention she's JUST as powerful as herself. Stripping her of her own powers would be impossible, since she had to use the elements of harmony themselves to lock her in the moon.
If you noticed, Discord was kind of destroying all of Ponyville, and he had the NERVE to be arrogant about it. Whatever happened, happened, and he was just as powerful, if not more than them. Again, they used the elements of harmony against him.
Kingdom almost entirely run by enslaved, helpless ponies to which she felt the need to save. She simply took down their ruler, to which he resisted.
There is no "real" villain in MLP, because, despite my earlier text, EVERYONE can be seen as "evil" if looked at from a different point of view. Why no mention of Changelings and the blatant racism against them? Why is it that Celestia HAS to control absolutely everything, even the celestial bodies themselves?
Celestia, at least, in the already set point-of-view for the show is not the villain by any means. Villains are villains for a reason, not because they're "born" evil. They did bad things, which makes them bad. Celestia didn't do anything but stop it.