Hi David,
When Networks for WordPress is activated only on the main site instead of on all networks (as far as I understand it, that does not affect proper operation) the network management page Network Admin > Sites > Networks is still visible on all networks. This means that a user that has been promoted Super Admin for one particular network, can now not only see other networks but even create new ones.
Would it be possible to NOT allow Super Admins of other networks to be able to do this? Either by not showing the networks management page (obfuscation) on networks where the plugin is not activated or adding a specific capability (other than manage_sites) that can then be limited for specific Super Admins using a plugin like Extended Super Admins.
In fact, the latter option, in combination with moving the networks management page to top level in the menu would in my view well suit the importance of the (core) functionality Networks for WordPress handles :)
Thanks!