I would, depending on my OP. The Templars are a cohesive fighting force, already trained and armed (I don't know yet that they've been infected with Red Lirium). The mages are a loose confederation of individuals with magic but no real experience in military strategy, etc. With regard to the breach -- suppressing its strength to match my ability to shut it makes a lot more sense than pouring more magic into it. Tactically, the Templars are the better choice. Politically, they are the better choice. Militarily, they are the better choice. And no, I don't want to stick mages back into a prison called a Circle.
The Templars being able to suppress the Rift was a big question mark and the mages have much more room for improvisation, they are not one-thick ponies like the templars are. Also, the mages did offer the alliance and the Templars were indifferent if not hostile to the Inquisition. So as the closing of the Breach goes, siding with mages seemed much preferable and at that point that was what the Inquisition was all about, nobody knew about Cory and his plans and his Venatori... so basically mages were better for the task at hand and easier to acquire... that is before time magic got involved and things got complicated, of course, but after that the choice was between two unfriendly factions, but still with one being unfriendly not by choice but by some strange Tevinter involvement possibly involving time magic. With addition of the fact that SOMEONE had to be responsible for the explosion, the matter seemed almost as pressing as closing the breach... Of course, the Templars were in the process of getting heavily corrupted right then and there, but Inqisitor didn't know that.
In my opinion going the mages' path and then conscripting them is the most logical thing Inquisition could do. Although I do understand your arguments. Still, they generally come into play only when you know you can get Templars to work for you (which was not sure), that their power would work on the Breach (which was somewhat questionable) and that there would be a military campaign ahead of you (which you couldn't know either). The one area where Templars definitely were ahead was PR - getting the order to work for you had potential to give you more credibility (as damaged as their reputation was) while working with mages could make people suspicious.
EDIT: Either way, I again got into off-topic discussion since nothing of the above has much connection with previous decisions of Fereldan monarch 
So, more on topic - while Templars might have advantage over mages when one fight the other, I'd be very cautious with saying that templars are a better possible addition to regular army. Basically, Templars shine against mages and in no small part depend on getting close to the latter. If you protect the mages well and treat them as artillery/support units, they can be devastating while the templars are just another well-trained and well-equipped infantry, not necessarily well suited for mass battles... It's still great to have them on your side, but the mages can make a much greater difference on the battlefield, if only you manage to protect them properly (especially by keeping enemy templars at bay).
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