To be fair, the Empire originally attacked the Republic for no reason other than to conquer them and take over. The Republic knew perfectly well that If they didn't wipe out all the Sith that they would seek revenge in the future.
That's kind of what Empire's -do-, though.
And you generally don't have to wipe out an Empire to keep it from coming back. If you beat them once you can beat them again. No reason to make them hate you.