you have to disable the mod when it gives the error message (not delete it), go into the mods page, and update. you can re-tick the disabled mod too at the same time. Press confirm, it'll update, then restart the game.
It's a bit of an annoying way to do it, but until we get a launcher that can update the game(steam already does this, but I don't use steam) and mods without loading the game, this is the best option we have.
So, you're complaining to the wrong person, Darkfrei, complain at the devs.