There is about a 99% chance that syphilis's answer covers it. But for the record, if the program spawned by the GUI is not so well supported by Perl as to have a module for it, then Unix::PID might be useful, e.g.

use Unix::PID;

my $ps = new Unix::PID -> new();

# wait for completion of GUI's subprocess
$ps -> wait_for_pidsof("name of program spawned by GUI");

# kill the GUI process
$ps -> kill( $ps -> get_pidof("name of GUI program") );
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Mac OSX conforms sufficiently to Unix for the purposes of this module, although the module documentation doesn't appear to give a list of supported environments.

Update: in a multi-user environment parents and children would have to be user-id'd and matched up before doing the wait then kill.