I'm afraid namespace::clean will only help with things in the current package. It won't help with reloading modules when they change. For mod_perl, we use Apache2::Reload to do that, and I think there are similar things for FastCGI.
The fact is though, all of this is a total hack. There is no way to reload modules built into perl, and none of the approaches people have tried to add on actually work for all cases. So, the best advice is to code differently for persistent environments like FastCGI and mod_perl.
I would advise you to offer an option that works more like the other FastCGI modules and like mod_perl handlers, i.e. it doesn't try to pretend to be CGI, so it offers the full speed advantage of a persistent interpreter. If you don't do that, your solution will always be significantly slower than mod_perl and PHP over FastCGI.