I see this working in a different way. Set aside the idea of players creating their own cards for a minute and just think about what moddability usually means. Think of games that have had a lot of support from modding communities now and in the past... Minecraft, Half-Life, Doom, etc. Each player generally isn't making their own mod; instead most players just play the game (and the mods) and a small percentage of players team up to create the mods.
It's up to the groups of players who create the mods to balance their own mods (and promote them, and so on). Sure, modders can have the ability to create a mod where the only card is the "I win" card, and whoever plays it first wins. But nobody would play that mod, so nobody would make it.
In general I think if you give people a nice foundation to build on and a lot of creative freedom, many of them will make things that are pretty cool, not things that don't make any sense. The best mods will naturally become the most popular, and mods that have balance issues will either get fixed or die.
Now, if we wanted to come back to players creating their own cards within mods, there are ways that could be handled (we can start another question for that), but we shouldn't confuse the average player having the ability to create cards with moddability. These should be two entirely separate things.
TL;DR: Mods are not the same thing as player-created custom cards. There is no reason to try to control the balance of mods, just let people do things however they want. If they make a good mod, people will play it, if they make a bad mod people will ignore it.