You should really consider using FastCGI. FastCGI keeps Perl and your program in memory, like mod_perl does. But FastCGI runs in a separate process, one per application. This keeps different configurations in different processes. You can even use different user accounts for different applications. A crashing application does not kill the webserver. FastCGI does not depend on one specific webserver, any FastCGI compatible webserver will do. Of course, FastCGI has the disadvantage of having several instances of Perl running instead of just one (so it may use more memory). And it has a little bit more overhead because it needs inter-process communication between webserver and perl, where mod_perl just calls functions.
Today I will gladly share my knowledge and experience, for there are no sweeter words than "I told you so". ;-)