Hey, Einar,
Admittedly, I haven't been in situations where that was an issue (I guess I've been lucky! users I've worked with know better) - but obviously many people have to deal with this.
Most of the apps I've been involved with were administered in such a way that users weren't permitted to touch the software area.
Admittedly my knowledge of this topic is pretty limited, so your best bet is to do searches on this site and other sites for more information on best ways to protect an app...and/or maybe someone else with more knowledge of securing an app can jump in.
Kevin