Actually, encrypting the JSON files sounds like a really good solution. Seems that Kyatric was working on something a while back, but it looks like that never got off the ground. Still, there are a number of javascript cryptography libraries which might be turned into a plugin.
Are you trying to prevent users from learning map secrets by reading map files? Or are you trying to make sure everyone is playing on the same map in a multiplayer game? If it's the latter, you can usually get away with a hash instead of full encryption.
Understand that you can't be entirely secure. At some point, you have to accept that your game is running on someone else's hardware. You can however, make it a huge pain in the butt to cheat, and encryption will accomplish this.
Ninja Edit: