I just finished my first play through as a warrior and I would like to try again as a mage. Can you side with the templars during the final act if your character is a mage?

I was certainly given the option to side with them, ultimately I didn't however it was a choice that I could choose.

Yeah, but you're an apostate....

I have thought about this when planning my second playthrough as a mage and I was thinking it would surely make no sense for the game to let you side with templars but I bet it does. 
 
Also yeah, siding with templars in the game seems like it might be hard if you want to keep a mage in your party...