I agree that its definitely not black and white. I just believe that the Republic is whitish-grey and the Sith Empire is blackish-grey.
Individuals can overcome their environments and be good or bad. And I can imagine an empire run by a non-Sith being successful and worthy of respect (Grand Admiral Thrawn in the distant future perhaps?) But the state of the Sith Empire at the time of the Old Republic, it's leaders promote an environment where evil can flourish and good is hard to come by.
It can be argued that the blatant evilness of the Sith Empire is preferable to the hidden corruption of the Republic, but that isn't my view.
I do enjoy the options presented in the game, though. My Sith Inquisitor is an evil **** and relishes in it. My Imperial Agent, on the other hand, is a consummate professional and is loyal to the Empire. She often times makes light side decisions if they help her mission and objectives. This puts her at odds with the many Sith in power, and I believe that is an accurate depiction of the flaws of the Sith Empire at the time of the game.
The Esseles vs Black Talon is an interesting example.