One possibility is to give gates a logic input they must receive to be brought online. If you want your gate to be open and known to the public, check the 'is visible to everyone' button (wherever it is decided to put that) and set up an activation block to keep the gate on at all times. In an emergency you can go to the gate and shut it down, but remember: just because a gate has no output, i.e. won't send players anywhere doesnt mean it can't receive from other gates. One gate can have multiple possible inputs, but only one output. At least that's how it works at the moment.
So in order to lock down your gate network, visit your public gates and shut them all down. The enemy can't use the gate until they destroy the faction module and reactivate it. If they accidentally the whole gate computer, sucks, they broke the link. You can keep hidden warp gates enemies wont know about without scanning, and require a logic gate lock be activated, or go through the process of destroying the faction module again.