Molock

If you go by how the Jedi act and what the Sith teach they are technically on the wrong sides of the war.

the republic values personal freedom above all. The Sith code is all about earning ones own freedom through gaining power. "Peace is a lie, there is only passion. Through passion, I gain strength. Through strength, I gain power. Through power, I gain victory. Through victory, my chains are broken. The force shell set me free." They even encourage their apprentice to eventually kill their master in order to prove that they are ready and strong enough to be their own master. Thus sticking true to their code of earning their freedom through the power of the force.

The Jedi on the other hand should be on the side of the Empire. It's not so obvious as with the Sith, since it's not really tied to their code per-say, but more so in their actions and teachings. They have a strict cult like mentality which is enforced through brainwashing. They take force sensitive children when they are young and impressionable then proceed to brainwash them into being slaves to the established authority. They teach them that all emotions are bad and you should strive to be emotionally disconnected from everything and mindlessly following the orders of your superiors without question. The Empire is all about following strict rules and following orders. Since in the Empire you are so often ordered to do some pretty messed up things you pretty much have to force yourself to be emotionless and all around disconnected from the world in order to cope with it all. So that perfectly fits with the whole no emotions thing that the Jedi teach.