Yes, messing with the system perl can result in an unstable machine. If you took a backup before doing this, now is the time to restore. If not, consider this an unfortunate lesson. Backups are a good idea.

The first thing I'd suggest would be to go down the Disk Utilities -> Repair routine, let the system determine what permissions things should have, and reassign them accordingly. If that does not work I'd suggest looking at using Pacifist and restoring these files:

"This is useful, for instance, if an application which is installed by the operating system becomes damaged and needs to be reinstalled without the hassle of reinstalling all of Mac OS X"

For future reference the XCode alternative I mention can be found here.

Update: To address your questions in the CB regarding the installation of your own Perl elsewhere on the system (which is a good idea), http://perlbrew.pl removes some effort in installing and maintaining Perl (or multiple Perls) on your system. It can also be used to automate testing your code against multiple versions of Perl. That said, the README has an explanation of the 3 lines required to install Perl to a path of your choice. See also INSTALL.