Ea : Well, sort of. You had to choose an alignment before selecting an AT. Now you select an AT, go run the co-op tutorial, and decide on a starting alignment in the tutorial.
To clarify, with Freedom: once you have run the tutorial at least (some number of times, perhaps once, on an account), you can choose to not play the tutorial, and choose to arrive in Atlas or Isles (for non epic archetypes, and for non Praetorians). This gets you there at lvl 1. The tutorial lets you decide too, and you arrive at level 2, with a few more inherent powers and the like.