The mages seceded from the Chantry, which controls the templars. The templars had never existed as an independent polity (they were the Inquisition when they were independent) and had no claim to authority over any mages of their own right. There is no possible moral excuse for waging this war, and there are no good points to the Order as it stands now.
This is untrue. The Templars had - long ago - existed as an independent party and bent to the Chantry's influence when the Chantry controlled the mages. Granted, even if the Templars had stayed with the Chantry, there is no reason to believe the Chantry was going to be all, "Cool! Go be free, Mages." They would have likely sent Templars.
Disagree with the Templars breaking away from the Chantry if you like - the Templars perhaps waged aggression against the Chantry - but the Mages were as aggressive, if not moreso for being first.
The Lord Seeker and Knight-Vigilant are both subordinates to the Divine, not independent actors.
Not precisely. They are the Right Hand of the divine, yes, but the Templar order is the remnants of the former Inquisition, as are the Seekers, and joined with the Chantry in the Divine Age under the Nevveran Accord. Their independence is either equal or less an act of aggression to the Chantry than the Mage's independence, depending on how you view it.
As the Inquisition, I intend to handle the protection of mages myself, and will do it better this time.
So one person will be in charge? That's great checks and balances.
And this makes me LOL particularly because the Templars basically came from the last Inquisition. You would make yourself the Templar. What an interesting choice. When innocents are slaughtered by abominations that were once weak mages, when blood magic runs rampant, when demons are called into villages and you see the harm first-hand and can only do so by some means of controlling the mages, what will you do? Will you let it continue? How will you stop it? I am not saying there aren't better ways than the current Templars (I'm adamant there are), but I do think there are a lack of easy answers.
Maybe they can be Grey Warden conscripts, but I'd be reluctant to suddenly bloat the Wardens with an ideology so slanted. Of course, anyone who leaves the Order before the war is over will have more options...
So maybe they can all be sentenced to the taint and potential death? Just because being a GW worked out well for the PC in DA:O doesn't mean it usually does. That's a pretty cruel sentence to place upon Templars wholesale.
Hardly. A righteous war needs not have all its warriors be righteous; that's virtually impossible. There's been plenty of wrongdoing by mages, I won't deny that; it's just that none of it changes the fact that the Templar Order must be destroyed, and the Chantry prevented from recreating it on similar terms.
You have come up with no better solution. Your whole, "I'll keep mages in check" is not a solution that makes any sense in the lore of Thedas. What happens when you, as the Inquisitor, die? How can you be everywhere? Without a solution, the Templars will have plenty to join their ranks and cause and the Mages may even be hunted and lynched and so forth, plus many commonfolk will die at the hands of mages and templars alike. You have presented only criticism and no solution, with no understanding to the problem Templars were created to solve. You acknowledge it exists but have no desire to solve it beyond a vague, "Well, I'm trustworthy, I'll handle it." You don't even have a code, like the Order. You have nothing.
I am not suggesting the Templars are righteous. I am suggesting they are the product of a problem that requires a solution; I am not saying the Templars as they are today are that solution, but I am suggesting there have been far worse solutions in the past and that having no solution is also far worse. For all involved. This will get uglier before it gets fixed, no doubt, but the idea that it is black/white will not fix it sooner.