Before launching the game, manually delete all mod content and all references to the mods:
1. Go to [Path]\My Documents\My Games\Sid Meier's Civilization VI\Mods and delete all files there.
2. Go one folder up (should be something like [Path]\My Documents\My Games\Sid Meier's Civilization VI) and delete "Mods.sqlite"
3. Go to your Steam Library, right click Civ VI, choose Properties, Local Files and then Verify Integrity.
At this point, the game should no longer recall any mods that you had and any game files that might have been modified by an ill-behaved mod should be restored to their original, unmodified form.