Yes, it's possible to switch sides from Freeport to Qeynos, and Qeynos to Freeport, providing you are in the level range it requires (believe its 15-19). It begins at Stilus Graphium who is in East Freeport.
Though I've never done it to confirm its accuracy, this
link is great stuff. Or looks to be. Explains the whole thing from start to finish :) Hope that helps!