I don't think you can do what you are thinking of doing. You could make an application to run PERL scripts FROM Media Center, but there's very little you can do to actually 'automate' Media Center, unless you want to generate keystrokes and/or mouse movements.
But there is potential for things like file conversion, getting data etc. using PERL scripts (loading data from PERL scripts is the next feature I'm adding to Yougle). You'd have to do that by executing the scripts (and the PERL interpreter) from your C# code.
By redirecting the text output, you could construct progress bars, informational displays etc. But there would have to be a reasonable amount of C# / MCML code to support your PERL.