Although I understand where Google is coming from, I also believe it is unreasonable to force all Chrome users to obtain extensions from only Chrome's Webstore and to force all of the other businesses to include their own extensions in the webstore in order for Chrome users to have continued access to their services. I have an idea that might resolve the issue.
Why don't you arrange it so that users will get an email informing them that the extension has been disabled. The email will include a link to a secure page that can only be accessed through that email link. If the user wishes to enable the extension, they can do so through the secure page that the link will take them to. If they don't wish to enable it, they would just choose to leave things as is. It would be similar to the process used when someone forgets their password and needs to reset it. After all, the process is deemed secure enough to recover passwords.