If you don't link to the other perl you just have to call it from your scripts instead so-

#!/usr/bin/perl

becomes-

#!/usr/local/bin/perl

moo@cow[58]~>/usr/local/bin/perl -v

This is perl, v5.10.0 built for darwin-2level...
[download]

Or /opt/ or wherever you put it. I think. If I'm wrong someone will likely correct me. In the sysadmins and masochists I mentioned before, I'm pretty solidly in the second set. :)