The Sith want to exterminate the Jedi/Republic (and have tried many times in the past before this war) just as much as the Jedi want to exterminate the Sith, because they're butthurt over the fact that they lost the previous wars.
The Jedi want to exterminate the Sith Empire, who have oh, I don't know, murdered countless civilians, bombed and desecrated Coruscant....attempted to destroy their homeplanet...in the JK storyline the Sith Empire destroy an entire planet full of innocent farming civilians for the lulz.. It doesn't help that every Sith is a slave to probably one of the most evil beings in SW history (who, If you didn't know, has the ultimate goal of exterminating all life in the universe, that includes everybody in The Empire)
Seems pretty fair to me. Also, what do you think The Empire are going to use the foundry for? Making protocol droids?