The timeout settings Jason mentioned are a good idea.
Another one is don’t run the installer from the __Download folder… but at the same time, I actually prefer to run out of that folder most of the time because cleanup is handled for you.
You can set a custom timeout for each run or wait command that is different than the global one, and that is the best option in addition to setting a much longer timeout globally.
Killing the installer that is running and stuck or rebooting the system is really the only option. If you can run actions through BigFix through another site, then you could use BigFix to clear this, but if the action is stuck in the running state, then you probably con’t use BigFix to clear this.
Related: Actionscript Wait timeout on hanging process - #14 by JasonWalker