Most of the trophies will be unlocked naturally. The one thing you shouldn't do is destroy or corrupt any shard throughout the whole game.
After beating Legion and Salvation, a black portal will appear below the Skill Tree in the Sanctuary. At this point, do not go through the portal yet, you should focus on finding all perks, and all seven Elder shards.
Mince you have those, backup your save file, then proceed to destroy or corrupt all seven shards. Once this is done, go through the portal and beat the boss. Once you finish the game, backup your save, and do the opposite of what you did before (destroy or corrupt), and go through the portal again, beat the boss, and that's it.