It seems to me that it may make sense to create a Perl wrapper for whatever program you are using. Have the wrapper open up the file handle to the piped process, then have it listen on a socket of your favorite flavor. Have your main program open up the socket, and when the connection is closed have the wrapper exit. If it still hangs, send the pid (in the special variable $$) over the pipe after opening the socket, and kill it by Pid.
Out of curiousity, have you set $| = 1;? Also, is the program you are piping to Open Source? You may be able to create a full fledged wrapper if it is (i.e. use Inline::C to compile the program in a way you can call) That, or you could change the program to listen on a socket. Although, that might not be as easy as a wrapper.
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