How do you want to Prevent mods from deactivating Achievements.
If you would download this mod and run it it will only cause your game to create a modded Batch of Achievements wich are completly separate from vanilla Achievements

True, so it only works for modded games with the achievements for modded games.
If you don't care about the achievements you can just do
/c game.player.force.research_queue_enabled = true
Personally I just don't like disabling the achievements with executing a command, even if it's not really a cheating command like this.