Only useful thing i can think of is to use the protected card as to only boot on second slot, or use with only SMS or HDproject :)
The best protection anyone can provide is educating the user the importance of the save files and not to delete them.;)
If they continue to delete them and your the one who has to keep re-installing it back for them...make each time a little longer before re-installing and they will learn what its like to not have it at all....but of course its up to you on how you handle your family and friends in this respect.:p
The best simple protection i can think of is the very old and basic BACKUP.
uLE can do it with copy and psuPaste in to a pen drive.
If some one delete the essential files, just restore it.
I'm taking about a method that makes that anyone copy the 3 filer óf the installation.