I think most pro-mage players understand the need for mages to be properly trained on the use of their powers, but the dichotomy is whether the Chantry and the templars should have authority over the mages.
Having a religious organization that pretty much vilifies mages and magic, to the extent of Andrastians killing mages for things they didn't do (as Wynne discusses with the mage protagonist when she addresses how mages are killed outside the Circle), isn't something I condone. In fact, Lambert comments on this towards the conclusion of Asunder. "Without the templars, the Chantry was toothless - nothing more than a bunch of old women armed only with words. What would she do? Try to convince the people, after ages of teaching them mages were to be feared and contained, that now everything was different?"
By your own admission, what the Chantry teaches is that mages are "to be feared and contained" rather than killed
Now, this need not be a vilification. If all that the Chantry teaches is "magic is dangerous, mages can kill you with their mind, mages can be possessed by demons, mages once enslaved the whole continent", then all that they are doing is telling the truth.
Naturally, some people will react drastically to violently to this and kill an innocent mages but the responsability for that rests solely upon their shoulders, not the Chantry's.
What would you have them do? Keep the truth from the peope?
While I believe that mages need proper training, I don't think the Chantry or the templars should have complete control over the mages.
They don't. Mages have many rights and freedoms the Templars are obligated to respect.