You don't have to really worry about this trophy until Act Three.
During the final quest 'The Last Straw', you absolutely must side with Meredith and get rid of the mages. There will be a few other conversations with Meredith after the initial choice, but they don't seem to affect anything.
Once you've fought all the mages and defeated the final boss - there'll be two cutscenes. The trophy should pop around the second cutscene.
Any decisions during the quest do not affect either the Mage Hunter or the Arcane Defender trophies.