ClickOnce handles updating an application very well. I don't see a problem here, if the user finds that the application is not working (because you have made a change server-side, that warrants them to update the client), they will restart the application and be prompted by the ClickOnce update mechanism to say an update is available (if this has been set up), once the application starts again.
The only way you could tell whether the application was due for an update, whilst the application in question is still running, is to poll the ClickOnce deployment file on the server and compare the version number against the current deployment. Not advisable.
Edit:
Another way to ensure that your users always have the most up-to-date version, is to not include a persistent deployment file and make the user always run from the launch page on your website. This would only dish out the latest and greatest version.