Not exactly- You choose which faction to play as at the start and can switch mid game, yet for some reason some maps only let you play ones from certain timezones. Its been along time since i played, so i can't remember the exact ones. You choose on Instant action ofc, i.e
Map A- Conquest, Galactic Civil War ( Empire vs Rebels)
Map B- CTF, Clone Wars (Republic vs CIS)
Map C- Conquest, GLC OR CW.
But you can't mix the sides up, as if to have Empire take on CIS so to speak. I can assumes theres mods out there for the PC that let you do that, but i'm a console man