What's the biggest problem the mages have? The Templar leadership have their heads firmly up their own butts. What's the biggest problem the Templar have? Same. Right at the moment where the inquisitor makes the choice, the mages may be the more inviting opportunity, but the Templars are the real problem that need to be fixed if an end is to be put to the civil war. Based on what my character knows at that moment, if the mages join the Inquisition, the civil war will continue, only now the Templars will be attacking the Inquisition. If on the the other hand the Inquisitor gets the Templars, the civil war can actually be ended and I can get the mages help as well.
Now that's wrong of course, but it's wrong because of things that the Inquisitor can't know at that moment. I mean, seriously. Time travel? Who sees that coming?
I think your reasoning is off. The templars are divided, something the Inquisitor can see early on without yet picking sides, but
Getting rid of the bad eggs who are dividing the Order isn't going to stop the civil war. It's just going to leave them more organized to go after the mages more effectively instead of it just being the mooks who disobeyed orders to go hunting mages on their own, (which the player cleans up in one of the early quests in the Hinterlands anyway).
The mage's biggest problem isn't that the templar leaders have severe cranial-rectomitis--they do, it's just not the mages' biggest problem--the mages' biggest problem is they can't sneeze without the templars immediately going all 'kill kill stabbity' on them.
At least that's how my Inquisitor viewed it anyway.
Ultimately, picking to aid the mages is the only way to end the civil war, even if you do make enemies of the rest of the order. The only way the order will ever stop persecuting mages is if you change how they think and wean them off the lyrium. And that is the Chantry's doing with their indoctrination, addicting the Order to lyrium to control them, and the result of centuries of anti-mage propaganda, not
This is evident by how easily
And, in any rate, not something that can be overcome in the pace of time we are afforded for the game. It may take decades to undo centuries of prejudice/hate. And the good PR mages can get helping
may do more for them in the long run than stopping a few templars from poking them with sharp, pointy objects, which would be (from my perspective) a short term solution at best since, inside of a generation, the leadership will be changing hands anyway.
Using spoiler tags as this is an origins thread and trying not to spoiler Inquisition for folks who haven't been reading up on it or played it yet, major spoiler under the tag for Inquisition.
Frankly, I would have preferred an option to recruit both sides. That may have made for interesting evenings in the fort, but it would have ensured all involved were working together to solve the crisis and would have done a lot more toward ending the mage/templar conflict.