you can play through facebook or through
http://www.earthempires.com
both will work the same way, same codebase and have generally the same design.
you will be able to link your current account to facebook or use an account created on facebook to play from ee.com, it will go both ways.
and yes, Facebook will be launched pretty soon. I'm working on the new public re-design right now and it's coming along nicely. The other pieces are all in place, I just need to start tying it all together to make a good user experience, and we need to do a little more work to prep for new users and help them figure out the game from scratch :)