That's rather frustrating. I don't mess with files in the protected areas often, but I have occasionally had need to. As far as language installs (not just Perl), I've started using the various tools (perlbrew, rvm) that install multiple versions into /usr/local.

You can always install VMWare and develop on a linux install... I've been leaning that way lately anyway, and when I finally have to upgrade to El Cap (I have Yosemite at work and Mavericks at home) I'll probably move even more in that direction.