deactivating = not loading extra code?
Yes, that’s correct. Once a module is deactivated, its code doesn’t run on your site.
global control for multisite mode. it’s cumbersome to have to go through each site to set up jetpack.
That’s indeed something we’ve considered, and started working on. Until we implement more options in Jetpack’s menu in Network Admin, I’d recommend using the available filters in your own little network-activated plugin to configure and customize Jetpack on all sites of your network at once:
https://jeremy.hu/customize-the-list-of-modules-available-in-jetpack/
consider the module of private site. I know there are great plugins out there, however, i believe it’s a must feature for jetpack.
By “Private Site”, do you mean a module that would restrict access to logged in users only?