Depends on what the target machine is. If it's windows, it's possible to compile your source into an exe, and then use one of the available Exe encrypters like ASPack/ASProtect/Armadillo/etc which give you a pretty high level of protection even against Reverse Engineering (altho nothing is unbeatable).

About updating the 'Appropriate fields in the installed modules', I'm not 100% sure how this would work. Most probably needs editing of the modules, and some checks that are performed at runtime if a given feature is enabled or not.

Emanuel