Have smarter users. If your package breaks because it depends on trivial code which got deleted, you shouldn't have depended on that in the first place.
Preventing people from deleting their code -- always, or even just sometimes -- was never the right solution.
I know "have smarter users" sounds like a joke but a lot of the problem really is cultural. In most languages you would write a two line leftpad function, in the js world everyone will tell you you're doing it wrong and should use a library.
Have smarter users. If your package breaks because it depends on trivial code which got deleted, you shouldn't have depended on that in the first place.
Preventing people from deleting their code -- always, or even just sometimes -- was never the right solution.