Whichever direction you link it, that would seem to present a problem. If you're installing a separate perl because you want to leave the stock perl pristine for the OS to use, well, the OS will expect to find the stock perl in /usr/bin/perl. If /usr/bin/perl is a link to /usr/local/bin/perl (or wherever), then the OS will be using your local version, so you might as well have just replaced the stock version with your own version, right?

Another thought: if you symlink /usr/bin/perl to somewhere else, can you trust that an OS upgrade of the stock perl won't clobber your symlink?