I haven't done it, but allegedly, you can compile it in a different directory.
My perl on my box is in /usr/local/bin/perl. Perhaps you want to compile yours to either somewhere in /usr/local and then adjust your scripts.
I have glanced thru several books and not seen anything regarding this, however we just installed a new mail server that bundled an older version of perl in it.
They placed it in the home directory for the mail account i.e. /opt/users/mail/bin/perl.
HTH