With the possible exception of Jifty, I think you'll find that Perl MVC frameworks don't paint you into a corner. MasonX::WebApp, CGI::Application, and Catalyst are all totally ignorant of your model and just barely familiar with your view. (MasonX::WebApp expects you to use Mason for templates; the others work with anything, including Mason, for templates.)
All that these tools do is map URLs to method calls and provide some infrastructure for the web-specific parts of the input and output. Otherwise, they stay out of your way.