Core perl is installed in /usr (i.e. binary is /usr/bin/perl). By default all ports install themselves in /usr/local (i.e. binary file is /usr/local/bin/perl). After you install perl from ports it will optionally offer you to run a script which makes perl from port a default (it removes /usr/bin/perl, makes symlink from /usr/local/bin/perl to /usr/bin/perl and does some other things I forgot). So answer is yes, perl installation from ports will not interfere with perl installation from core unless you want it.
P.S. This information is correct for FreeBSD 4.x only. In 5.x they have removed Perl from core and it is installable from ports only.