Wow, I has the exact same issue as we speak.
It does feel like there should be some sort of automated notification option that is triggered after a defined time that lets the end user know there is a pending update, and for them to quit the application. I have, however noted that sometimes a quit does not equal a resolution to the update conundrum. I think, and I am unsure if this is truly the case, a restart may also be required.
The tricky thing is there is still a lag on the actual updating process, and due to that the end user being unawares of the process, the application in question can be relaunched prior to the update actually completing. Rinse repeat.
So I think the resolution should be a notification, with a confirmation of a forced update.