I don't think this is always the case with SWTOR. For example, in the Sith Warrior storyline whenever I faced Jedi it was very clear to me that they were the good guys and I wasn't. When the Sith Warrior fights against rival Sith, yes, then the enemy is evil but even in this case it's evil vs evil.
Thats not from my experience. The jedi you meet a self righteous douchebags with a few showing a whole lot of hypocrisy. Neither side are the good guys and neither sides are the bad guys.