If the user has a Jetpack widget active when they deactivate the plugin, the user will lose the Jetpack widgets they are currently using. We should check if they are using any of the Jetpack widgets and if they are, we can warn them: "Widget Foo is part of Jetpack and is currently active on your blog. If you deactivate Jetpack it will stop working. Continue with Deactivation / Go to Widget settings / Cancel"
Original trac ticket:
Closing this as wontfix as it's common behaviour for all plugins, and also happens when switching themes.