That isn't really a realistic solution if you also want to support the mod ecosystem (which IMO is much more valuable to a game's community than the potential downsides)
Ok, but the mod ecosystem is a separate discussion. And even if you do want the mod ecosystem, you can distribute mods as client add-ons so the mods can be evaluated independently of the host server.
Which is exactly what Gmod did, and they have this problem.
Just make mods opt-in. Vanilla servers by default.