Do I think he'll question the Inquisitor's decision? Absolutely, but then I think he would probably question it if you sided with the Templars are were behaving too balls-to-the-wall hardlined as well.
If I recall what the devs have said correctly, we'll be questioned on the "why" of our decisions a lot when we get back to Skyhold, and our conversations about why we did or chose something will/should have repercussions with them, both approval & romance-wise. So I think he will question not only that decision but others, but it will be our reasons that will cause him to like or dislike the decision we made. In regards to this particular choice, he may even be leaning pro-mage and get more riled if you choose the templar side.
I really like that the "why" will come into play with our companions, because we hardly ever got to explain our reasoning behind making certain decisions.. we just did or said something and our companions reacted to that. I'm sure there will instances of that as well but I do like that we'll be able to say, "Hey, I sided with the mages but kept *some* oversight for them because they could actually grow and flourish if they weren't kept under a boot heel all the time," or even, "I didn't really care who I sided with, I just want that situation over with, I'm sick of hearing about it!"
Being questioned about our motivations back at Skyhold also lessened a bit of my apprehension in regards to advisor romances - they'll still be in the thick of things, asking about your latest quests/missions when you get back, so there will be many chances to speak with them and build relationships.