Yeah that's totally fine. You don't have to solve the conflict between mages and templars to make them work together. Just make them sit down and realize how big the threat is. They can go back to slaughtering each other once the threat is dealt with, and you can tell them that outright.
This is one reason I was pissed I couldn't recruit Uldred and his abominations instead of templars/mages in DA:O for example. Darkspawn are more important, and logically Uldred wanted to talk civil at first, he could go back to his domination plans once the blight was dealt with.
Point: You missed it. 
We have to start somewhere. Why not now? Why not at a time when these two polarizing groups have every reason to work together as equals?
You accused me of being naive by wanting both groups to act like grown ups for a few minutes. I was pointing out that I didn't think world peace was going to happen overnight. I did say we need to get the groups to sit down and actually talk to each other. You know, instead of talking at each other?
Oh and don't put words into my mouth. I would never say, "You two can go back to slaughtering each other after this is done." If that is even an option and I hope it isn't.
If given a choice, I would say, "We need to start a discussion now on how to work together in this time of trouble. The conversations that could happen here could benefit all of us as a whole."
That's my choice and that's what I'd do. If you think it's silly or naive, then you're welcome to your opinion.