I forgot to clarify this in the OP:
This functionality would ONLY work in instances where the PDF is in use by another Adobe program. It would not apply if the PDF were opened by another PDF viewing/editing program outside of the Adobe family.
In those instances, you're on your own to close and re-export.
It's not quite what you want, but in CS6 the export dialog remains open while you find and close the offending PDF window.
I too find this very annoying. Not sure if there is a real full on work around since I might be saving to a shared folder on a network where the PDF is open on a different computer, I get this. I also get it if I drag a PDF to a mail window to send and then I notice I have to change something so I go back and try to save the PDF again over the old but it thinks it's in use just by sitting in the mail window. So I have to go and delete the PDF from the mail window, but it usually still think's it's in use. I then have to manually delete the original PDF and save back into the folder and then drag back into the mail window.
This problem is subtle, but I believe the general concensus is that it is
Mail.app's fault and there's not much ID can do about it.