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.
Ah, but can't you use that same justification to totally exterminate all enemies? Because if you don't, surely they'll eventually just start fighting you again?
It's an understandable justification, but rarely a very grounded or moral one.
For me, I've always viewed the Jedi Order as inherently leaning more towards what one might generally agree to be a moral good. It's never perfect, and trying to teach people to be paragons of morality from childhood has... not always resulted in the best outcomes. But on the whole, the Jedi tend to go for the whole "let's not be absolute jerks to everyone" and "I think some amount of self sacrifice might lead to a more acceptable world" sort of gooviness than the Sith.
The issues of rigidity, self righteousness, uncompromising world views, and just general stuffiness are real and worth point out too. These things also tend to lead more towards the whole "crusading, slippery slope dark side" sort of fall too.
The Sith on the other hand... well, they're basically out to manufacture a bunch of sociopathic psychopaths. While the Jedi teaching might lead to this, the Sith sort of have it as a stated goal. This doesn't mean that Sith are any more inherently "bad" than Jedi are inherently "good," and certainly "good" Sith are not a theoretical impossibility, but... well, the Sith aren't very big on being generally swell people unless they'd be too much trouble to just kill off.
When it get's right down to it, Jedi generally try not to be jerks, and Sith... don't. But the Sith don't always see being a jerk as the end goal, it just sort of tends to... happen. That's about a morally clear as we're going to get on the issue.
As for the civilizations they support, they can basically go either way. The Empire was way more ingrained and social acceptable/mandated racism and so forth, but societies are quite capable of manufacturing a whole range of people and personalities, and there will always be those who are able to be "good people" in the mist of otherwise reprehensible behavior.
And no such thing as black and white, blah blah, shades of gray, yadda yadda. The core of idea of this topic is basically the fundamental questions of right and wrong, social justice, and society that people have been arguing about forever.