I guess it really depends how you want to use the tool. There are a lot of powerful tools in the world (not just in programming). You (or some organisation) can choose whether the tool is your slave or master.
Some people *want* the tool to be their master. Whether you or I think that's a good idea, it's obviously a very popular approach - it basically sums up Java (or at least the popularity of Java, although things may have changed somewhat). People have large legacy code bases of Perl and programmers who are used to the Java Way trying to maintain it. TIMTOWTDI applies even here. Why not let them do it?
But Perl::Critic is still just a tool. You can still be the master if you want. Set the rules up as you wish, and allow your programmers to break those rules at will (with sound justification of course). If they get annoyed with particular rules, turn them off completely! Or don't use it at all. You're the master.