In my game, the mages ended up enslaved to the Venatori and mostly wiped out. I doubt Anders wanted that. If you follow the mage path though, it really depends on the end-game's choices.
That being said, his plan was stupid but miraculously had a result he hoped for: a mage rebellion. If Meredith had any wits, she would have used the destruction of the chantry as support for further mage imprisonment; reducing Anders to a figure-head of the dangers of magic. Instead, she chose to execute every mage in the Circle and turned out to be a red lyrium psychopath who could jump 30 feet in the air and bring statues to life... Then, very conveniently for Anders, all the Circles somehow managed to rebel in unison afterwards.
The mages being wiped out is an acceptable outcome Anders perspective. Remember, Anders is focused on the immediate need to act, not the long-term. What was important was to provoke a fight, not shape it into one that he would win. Anders priority was the end of the act/dynamic of oppression, not the mages' survival.
Meredith's annulment and an absolute loss for the mages aligns for that. If every mage is eradicated, Anders goal for no more Circle oppression is reached. There would be no more injustice of oppression/containment if there are no more mages- hence, moral priority fulfilled.
Yes, it is immoral in other ways- but by Act 3 Anders is quite blatant in demonstrating that he only considers his moral priorities a limiting factor, and mage survival isn't. It's also short-sighted, because mages will continue to be born- but Anders short-sightedness was also established, as he has no clear plan or linkage of steps for how starting a mage-templar war will actually lead to his desired end-state.





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