Just wanted to mention your timeline is a little bit off. The first Jedi Purge pretty much starts after Revan turned to the dark side to start the Jedi Civil War(aka The Second Sith War). What Jedi survived that war were hunted to near extinction by the Sith Triumvirate(KOTOR 2). This was the first Jedi purge. The Exile and those she trained, Revan and Bastilla Shan were some of the like 10 that survived to carry on the teachings of the Jedi. The Sith also do not necessarily have to lose this war, there are hundreds of years in Star Wars timeline that this game can take place over. Before Darth Ruin appeared(1000 years before Battle of Ruusan and the 'spys' you mention), there is approximately 1600 years of untouched timeline starting 300 years after KOTOR 2. The Sky is the limit in regards to who wins this war. Or should I say battle? Because no side ever seems to win.
OT: This game can go in any direction story wise, as I said above there are hundreds of years of untouched timeline to use. I'm really excited to see where they will take this game. As far as adding new classes goes, I'm for it, as long as they stay away from the whole new class should be OP philosophy. With the balance that I've scene in game so far in beta and videos. I'm sure they could pull it off, same goes for skills.