Oh my god, one of the most stupid comment
While it may be the most stupid thing ever for you, other Jetpack users might find it logical that new features are immediately available when updating.
As I mentioned before, we did choose to make that decision for the users instead of introducing another option to the plugin, much like it's done for some of the core WordPress options that are sometimes removed. See #21307 and #21509 for 2 recent examples.
I understand your frustration though; in your case it would be better if new features were not automatically activated.
Luckily, there are quite a few solutions out there if you're not satisfied with Jetpack's default behaviour:
- You can use the Manual Control plugin, or develop your own plugin. Other users have already reported the Notifications problem to the plugin, and some of them shared a solution to the problem here. You could apply the fix they proposed, or propose a patch to Mark Jaquith to fix this issue.
- You can edit Jetpack's core files to deactivate the automatic activation. I wouldn't recommend it though, since your changes would be overwritten with each plugin update. An alternative would be to fork the plugin and install a modified version of Jetpack on your clients' sites.
- You could enable Jetpack's Development mode, thus deactivating all modules by default. That's a good solution if you don't use any Jetpack modules that actually require a WordPress.com connection.
I hope you can find a satisfying solution among these.