Cwd also exports (on request) a method called abs_path, which will convert a symlink to the real path. You could use this for your comparison, ie:

use Cwd qw(abs_path getcwd);

if (abs_path('/home') eq getcwd) {
  print "Correct directory\n";
  # do whatever needs to be done
}
[download]

Of course, substitute your symlinked path for /home in the above