I'm having real problems keeping control of this. I have deinstalled Jetpack because it is more of a liability than an asset on a single-user multisite installation, such as I have been setting up here http://Aerist.org . It would be helpful if it would have the option to share settings and data across all subsites, but it doesn't. And I have to deactivate the functions I don't want on EACH subsite rather than once globally, or perhaps activating them as they are needed on each subsite.It would have been better if each option had been made available as a separate plugin, actually. MUCH better.
I have just discovered you can install a plugin that stops new features being activated on install. It may also stop features on a new install, we'll see. http://wordpress.org/extend/plugins/manual-control/
So, a terrific idea, but I can't take the risk of a new feature just blowing everything else up.