The only two option would be too:
1. Hide the data/file. Since you probably don't want a rootkit with your game then you could hide your data in a format that the user couldn't easily understand. Or hide your files inside other files.
2. Encrypt the data on disk. Then decrypt the file when you want to read the data. I think the S plugin supports encryption or you could use Python to encrypt.
If you don't care about hiding and just want the user to not be able to change it, you could try a checksum. I think Minor or somebody else wrote a tutorial about. As anybody would say, all of these techniques are pretty easy to get around, but will work to keep your average gamer honest.