The issue that you are describing sounds like BatchPatch was not the cause of the problem but rather was a symptom of an issue that occurred with the operating system. This is why you had to reboot the system to get things working again.
Actually it was because of a faulty command file not having an end quote on the tail end of a wsus execute command with parameters. Once the problem was found, I had to terminate BP and run again. The question really is, Is there an easier way to recover from an execute error, other than rebooting everyone, i.e. halt BP, remove binding processes and re-run the command?
Generally speaking, a reboot shouldn’t really ever be required. As for some kind of “smother” way to kill processes, BP can only currently do this for processes it knows about such as for the Windows Update menu actions that are built-in to BP. But when you execute custom commands and/or processes, BP doesn’t really know what exactly it would need to be killing. You can certainly use BP to kill remote processes by name, but you would have to insert the names yourself.