The best hope is that by having them build parts of the same system in that multiplayer environment, that they'd feel enough ownership of the system not to wreck it all. I'll definitely have to put in a world backup system but the real limiting factor of any solution would be that python script access. I wonder if I could set up some form of authentication and logging so all scripts could be traced back to whoever runs them, I have little experience with Python but I guess the libraries are all accessible so it may be possible to just add it in. Actually: thinking on it, I could have a gatekeeper so they authenticate with my server which will then pass the connection on to the actual Spigot+RaspberryJuice server perhaps? Otherwise I'd have to modify the RaspberryJuice mod as well, which I suppose is just Java so I'm fairly confident I could do that... blargh.
Yeah, the joint ownership was what I was trying to get across. And setting up a simple proxy that logs who does what shouldn't be too hard, that way you don't have to add hooks to what's already there and can have it all in a central place. And nightly backups of the server shouldn't be too much of a pain and that way even if a troll does muck things up your students only lost a few hours of work.
There's plugins to auto-backup and do all sorts of world management; ultimately I want them to have fun making something, if I can teach them logic gates and programming then all the better. If I can teach them other things such as some basics of architecture or geography, then that's even better!