wpkg-gp doesn't have nay way to stop it....
what you could do is to set timeout on each command, by default that timeout is 3600seconds (1hour), but you can set the timeout you want on a per command basis
See:
http://wpkg.org/TimeoutsOn another thread on this same group: "
Set a limit on WPKG run on startup...", Marco Gaiarin documented a way to stop wpkg if it takes too long to run, but found that it works on the point that you get a login, but it keeps the hanging process running.
See: https://groups.google.com/d/msg/wpkg-gp/PMENkeCYzw8/cONPjIyGmjIJ
This issue has been discussed in the wpkg-users list, the final thought i get from that thread was that If you are having troubles with a package, the solution is to fix the package definition, not to set a timeout.
Another thing that was specified there was a way to check if there are updates, if positive then show a message to the logged on user and activate wpkg-gp on next boot; if there are not updates pending, then deacitvate wpkg-gp.
I'am testing that way right now, as we are having complaints from our users on the long startup time it takes sometimes...
It's not a solution, it's just a hack that get some better interaction with your users.
But if you have trouble with java, it's a sign that you did not tested every situation before getting your package definition to your users' computers. WPKG it's great, but you need to test a lot of scenarios before running it, even more if your installed base is so different.
Here, on my network we manually uninstalled any conflicting package before running wpkg for the first time, that was translated in eliminating the troubles with old jre, flash, and the like
I hope this helps