Thing is - the Sith are a ruling class, they are using the Empire to achieve their goals, sure. However, the Empire is not Sith. Just look at our average politician - you'd think your very own country is a tool for liars and hypocrites to become richer and to spread their economical and political influence beyond the borders of their country.
The backbone of the Empire are regular people. The game shows them as proud, sometimes arrogant, but also patriotic, loyal and brave. To me (and my grey Sith character) those people are the Empire, not the paranoid crooks who plot against eachother in dark tombs.
The Empire is a gun, the Sith are guys point and pulling the trigger. The gun has no say, while it may not be directly evil, it is an evil thing by proxy as it is being used for an evil purpose.
So putting armour piercing bullets in the gun (helping the Empire), is always a bad thing.