Capricorn! *waves* 
So, the Mage decision. Conscript.
I sympathize with the Rebellion. I really do. But it falls prey to the same failings in so many uprisings. Namely, that oppressed classes and people simply do not have enough people with experience in leadership and running a country/organization to have a smooth ride. If they had that much of a presence in the ruling class, they wouldn't really be oppressed.
So you have mages who have never had much responsibility thrust out in to the world trying to make it as a group. They have never dealt with this kind of situation before. Hell, compare the Templars' beef with Cassandra to the mages. The Templars are upset about the apostates wandering around camp and want to clamp down on them, the mages are complaining about their quarters because they're still gangly out of their gilded cage. Only a handful of mages have played politics, and even then, Circle politics or a court mage are far different than trying to negotiate safely for a revolution.
So I conscript, and then I push for mage freedom, but not willy-nilly. Let them grow into the responsibility by working with the Inquisition. I like Fiona well enough, but her signing up with Tevinter is just bizarre and there's still a part of me that headcanons that blood magic was involved on Alexius's part. That single move obliterates the Mage Rebellion's credibility in the entirety of the South, puts them into forced servitude to the Imperium, and there's the fact that a bloody Rebellion of mages holding Redcliffe Castle on an island in the middle of a lake should be able to hold off any Templar assault, especially when the bulk of their forces are on the other side of Ferelden.
*deep breath*
If they had had an Irving or the Hero of Ferelden as their leader, and the rest of them had grown up in more liberal, independent Circles that actually gave them some responsibilities, then the Rebellion probably would have avoided some of its pratfalls.
I usually Recruit the Templars, but that's because most of the jackasses in the Order are in the Red Templars, and Knight-Commander Barris is bae.
I don't mind Conscripting them either, mind.
INQUISITOR: Just...just *pinches nose* Just shut up and follow my orders for now, okay? We'll sort you out later.