I always felt the point of the mage/templar conflict wasn't supposed to be about Abominations. Or at least it shouldn't be. It should be about abuse of power.
You can see this in the history of Thedas. Abominations barely rate a mention. The big thing, the thing that got Andraste talking about how "magic exists to serve man, never to rule over him" was Tevinter. Its about people having unearned power and using that unearned power to oppress those who lack it.
Abominations fit in thematically quite well when they're the result of arrogance or recklessness, but I think one of the problems with Dragon Age 2 was that it went too far in turning mages into (to quote David Gaider) "a kitten that CAN EXPLODE IN YOUR FACE AND TAKE OUT AN ENTIRE CITY BLOCK IF YOU TOUCH IT". It just seemed like they'd turn into abominations at the slightest provocation, and this largely crowded out the other issue.
The theme of abuse of power is an interesting one, and one that follows quite naturally from the basic fantasy idea that magically gifted people exist. I don't think the exploding kitten thing is very interesting, particularly since it seemed to result in the discussions being about the frankly inconsistent evidence we have as to the likelihood of them exploding.
DAI does seem inconsistent with DA2, but I don't think it removes the case for Templars. Its just the case in DAI focuses more on the evil that mages do through greed or hubris. The case against mages in DAI isn't the foolish apprentice turning into an abomination, its Alexius and Corypheus and Solas. And I think its better for it.
I've probably been not so clear about this in the OP, but I by no means want mages to turn into abominations at the simplest touch. The theme of abuse of power is probably the thing I've been looking for, but couldn't find the words for.
However I'm not entirely sure I'd agree Alexius, Corpyheus and Solas are good cases against mages, as ridiculous as that may sound, since they aren't even remotely like your average mage.
That may have been arguably true in DA2, but I don't really see it in DAI so much. I wouldn't say the game is biased in favor of Templars exactly either, but the mage rebellion is pretty well shown to have had many negative consequences, and even fails completely, unless the Inquisitor happens to ally with them and maybe chooses Leliana for Divine. In every other case the Circles are reinstated. Anders' actions are widely condemned. The conclave explosion is the fault of a mage. The only major mage character who really argues mage freedom is Solas, who turns out to be a villian, planning mass genocide (as far as we know) when he brings the Veil down. The Warden mages fell to blood magic. Cory is a mage with a demon army who wants to rule the world as a god, supported by Tevinter supremacists, and put into play by another mage with similar designs to remake the world on behalf of elves (Solas). There was Alexius. You really think magic isn't still portrayed as something potentially dangerous?
The mage rebellion not succeeding is not something that I would consider displaying magic as something potentially dangerous. During war, there's always one side going to lose.
Some of the examples you provide were mages using desperate measures to attempt to counter the dire situation caused by external influences. Specifically the Wardens (due to the calling), Solas (due to the fact that his people were killed by an unforseen consequence of the Veil) and Alexius (due to his son dying from the Blight) and anyone can be dangerous, mage or no, if their situation is dire enough.
As for Corypheus mweh, on the fence about this one, I don't think it's solely displaying magic as dangerous.
More effective against what? It takes years to train a mage, and you have house and feed them, and supply lyrium. For something a little gunpowder could just as easily accomplish. Swords are arguably more common and numerous than mages skilled in magic, anyone could just grab one and try to stab people with it. Why don't they? Because most people aren't set out to just randomly kill and attack people for no reason.
When it comes to battle, the right tool for the job matters, depending who you are fighting and with what. Magic and/or ranged attacks aren't always going to the best or most efficient weapon in every situation.
But regardless that doesn't change the fact that this argument confuses morals with objects. Anything could be turned into a weapon, if the intent was there. This is the reason mages have to learn to focus and control their will, so they don't do things they don't intend by accident. Templars also spend a great deal of time conditioning their minds.
Magic has been shown to be effective against almost anything, because you can do almost anything with magic, it's the whole point of magic. Training doesn't really matter, it's about the potential. The use of a sword, shield, bow, axe, greatsword, etc. is limited by the tool itself. Gameplay wise the fact that mages are the squishiest of all classes is the counter balance to their damage and utility potential. (And even then, this counter can be bypassed by Arcane Warriors)
Either way I'm not trying to argue mages don't need to learn how to control their magic.
On a side note to add to this thread:
Since I didn't think the arguments being made are strong enough to pull mages back down from their favored position, I've looked for a poll to gauge how the general public viewed the mage and templar issue. And boy, do they favor completely free mages.
Almost 70% of players freed the mages: http://www.strawpoll.me/3269053/r
And about 50-60% of players choose Leliana as the Divine, thus disbanding the Circles: http://www.strawpoll.me/3269183/r and http://www.strawpoll.me/4977587/r