To be a mage do you have to be a rebel?
 

Is it possible to be a mage and work for the orcs? I ask because it seems that most of the mages are on the rebel side.

Well, you don't HAVE to. Since I played as a magician and allied with orcs in my only play through and I didn't have any problem or limitation that would bother me. But yeah, to learn some ( not very useful ) spells, you have to be high ranking ally for rebels I guess. Since there was no one among orcs to teach them.
But you can get mana regeneration regardless which side you take and that's all that matters for a mage in Gothic 3 IMO.

Where would you get spells from? Also, can you become a dark mage? You'd think it would be exclusive to playing with the orcs, because the rebels worship innos, not beliar.

You can get normal spells from Innos and Beliar shrines ( and from rangers for Adanos spells ), but to get the unique spells, you have to talk to certain people ( or maybe they get unlocked in the shrine themselves ) when your reputation is higher than a certain amount. Unfortunately, I don't know about them since as already mentioned, I allied with orcs.
No it's not exclusive to orcs, since hashashins also worship Beliar. There's a guy in Bakaresh named Tizgar who teaches this skill.
If you want information on trainers, look here:
http://guides.gamepressure.com/gothi…de.asp?ID=1958

I don't think the game ever makes absolutely clear whether siding with the Orcs is an action towards the middle Adanos(Xardas) path or Beliar.

Since you get your spells only from shrines you will be fine because whatever mage-specific skill the rebels can teach you you can also learn in the desert.