You can clone with
HTTPS or Subversion.
Because I am no guru with MultiSite, I have no clue how one might expect the force_activation and force_deactivation parameters to work in a MultiSite setting. There are currently no "bugs" with v2.2.0-dev in MultiSite, but these two parameters may function differently than what one would or may expect with the whole network wide vs. individual thing. Any advice here would be great, as I don't know enough about MultiSite to be able to intelligently discern whether or not our current implementation would meet expectations or not.
Shouldn't affect it - we're only using [de]activate_plugin() or [de]activate_plugins() (different functions) but not the [de]activate_sitewide_plugin() - so network-activated plugins shouldn't be affected.
When testing deactivate plugins, if the plugin wasn't active for the site, it was network deactivated. However I was testing as the super admin, so that may have thrown a couple things off.
When testing everything, it worked as expected so I am closing this. It was more to answer my questions (which have been answered through testing).