The only way that you can avoid storing the keys in the file system is that the program needs to be started interactively by someone who knows the key (password).

Since you probably want others to be able to run the program (either via web or command line), what you have to do is make one program be a front end to a daemon process which runs continuously and holds the key in memory (in a variable). This is quite non-trivial since you then have to make (and authenticate) connections to the daemon.

Although people (on slashdot, especially) like to point out the possible DRM abuses of TCPA and Microsoft's Palladium, it does have legitimate uses like solving this difficult problem.