Ok i see what you mean. Well ok indistructible or more durable Warp Gates are a bad idea indeed, but i cant see why it should not be lockable? I mean its my gate, so i should be able to decide who can jump through it. If not faction lock, see if this option fits more to your opinion:
The Gate is locked through a lock. You have to have a key to use the gate. Not a key you have to type or anything, a faction key. A random generated key generated when a faction is created. And you could get those jumpkeys by getting it straight from the guild leader or ones with enough permission to do so, or from any guild member whose ship you destroy. after destruction you could scan the wreck and get the key or something.
I dont know if its possible to make that happen, but its just ridiculous that i cant decide who can pass trhough my warp gate. i mean its no wormhole, its a machine which has to be activated. why cant i add permissions to it?
Farther i have to say, it would be better to have to activate the gate instead of just flying through. Like that, you have to lock on the gate and use an assigned key for warpjumps, than the gate activates and you fly through it. the activation could be made visible through an effect where the Inner gate would turn blue or something gatelike.
And for the problem with the attacks through gates, how about you cant build a gate inside of enemy territory. i mean you could build one a few sectors away, but then you could destroy it. If its not made more durable it shouldnt be that hard to destroy one gate.