Hey there. I found this for a friend just this day, thought I'd share it with you
http://www.qj.net/psp/homebrew-applications/xtreamlua-compiler-02-protect-your-lua-code.html
It worked for my friend, even when loading the Lua files into the actual server.
Credits;
Harry / Stoneharry - Tested it
Me - Finding it xD
Emeric0101 - Creating it.