I think you're safe with that setup. Unless you're particularly worried about mod_perl crashing apache. Assuming you use /cgi-bin for your current production directory, mod_perl won't touch your production code. Only scripts put in the /perl directory will invoke mod_perl.

At a later time you may decide to make mod_perl handle ALL *.pl|cgi scripts, but with THAT setup only files in /perl will be mod_perl'd.

"Falling in love with map, one block at a time." - simeon2000