I think the only really secure way to do this is to have a master validation server that keeps track of a checksum of every single version of validated missions. The first person to upload a specific mission name gains update rights for that file, which they can then pass on to someone else if they choose (or of course admins can change it).
Consequently the game will ask "Do you want to upload this?" whereas if the checksum isn't recognized, the game assumes that it's a user-made mission with the same name but it's not meant to be a version of the validated mission. Maybe it will pop up a dialog that says "Hey, the mission you're playing has the same name as this, might they be the same thing?"
With version numbers, it's all too easy for someone to open up the file in notepad and add 10 to the number, then resave the file and make whatever hacks they want. Granted cheating hasn't been a big problem that I'm aware of, but it does seem more than a little insecure and a really tempting way to screw up other people's saved missions. And it's inherently infectious - if one person joins a game that has the hacked mission file, leaves, and then joins another game, everybody else will download off that guy. Then they leave and go on...etc etc.
Plus somebody might tweak the mission for their own custom purposes, but also increment the version number to mark it as different. Then somebody joins his game and 'updates' their copy, and the illegit version gets spread and wipes out the original.
EDIT: Master "validation" server also doesn't have to actually validate every mission that it comes in contact with. It could just be a DB connected to Freespacemods.