was thinking about this a bit. Only things I could come up with was to check to see if there are command line switches that you can hand off to the GUI program that will give you the behaviour you want. I am guessing that there probably is not. (I think a previous poster mentioned this, so nothing new here)

The other thought I had was to keep track of the process id AND the lock state on the file that you hand to the GUI program. My thinking is that if the GUI program is modifying the PDF file you have handed it, it is probably locking it until it is done processing. If that is the case, you might be able to issue a kill to the pid after the lock is removed. Am not sure of how OSX keeps track of processes, or how you kill them off.

Good luck! :-)