I don't know if this suits your particular purpose, but another option is to prevent your Today extension from appearing in the Today center by calling setHasContent:
let bundleId = "com.mycompany.myapp.today"
NCWidgetController.widgetController().setHasContent(false,
forWidgetWithBundleIdentifier: bundleId)
It will still appear in the Edit screen, and users who have enabled it will still have it enabled, but you can hide it this way until you're ready to show it again, either in a later release, or perhaps when some dependency becomes available.
You can call this method either from the widget or your app.