I'd probably be inclined to keep the config as a perl hash in a separate file and build an admin facility that allows the editing of the variables in it.. see Modperl Guide - Writing Configuration Files. This has some great stuff even if you aren't fortunate enough to be using mod_perl.

At the very least, and for minimum extra effort for where you are now, write another sub that returns a hashref of all the config variables. At least that way you can let MySQL fetch them all in 1 query.

cheers,

J