Like other MMOs, The Old Republic will have two factions-the Galactic Republic and the Sith Empire. It was a choice they made early in the development, as explained by Daniel Erickson, the head writer for Star Wars: The Old Republic, in this 2008 interview: It wasn't until after the events of SWTOR that Jedi became synonymous with 'good guy' and Sith with 'bad guy'. The Galactic Republic call their force users 'Jedi' and the Sith Empire call them 'Sith'. There are dark side and light side force users in both the Galactic Empire and the Sith Empire. These stereotypes persist until they become cemented in the vernacular you see in the movies.
Winners often define our view of history, and so paint themselves as absolute good while painting the enemy as evil.
Also, the Galactic Republic is seen as good guys primarily because in the end they win. While the Imperials are far more 'Evil' in their practices, individuals may or may not be truly wicked or even dark side. This organization is what exists in SWTOR. But you must remember that originally the Sith was an empire, an institution that existed with formal structure. In the main Star Wars universe (that is seen in the movies), Sith is the opposite of Jedi. I think the confusion comes from the difference between the Sith Empire as an establishment and Sith as a practice.
