It is an interesting idea in principle, although I can see a couple of issues. Firstly is that beam armed ships wouldn't have much trouble destroying them with no downside whereas missile ships would have to use up a lot of their ordnance. Secondly, with that in mind I would damage every jump gate in the Empire to within a couple of points so I could destroy it whenever I needed to without any trouble. If I avoided that by preventing damaged jump gates from working, then I could still prevent an alien attack by damaging them slightly.
I do like the idea that they could be destroyed though so there must be an alternative that makes it possible but difficult. Assume that a jump gate somehow binds with the jump point, keeping it open at all times, and becomes more than just a physical structure you can shoot at. Perhaps jump gate construction ships could undo the jump gate or perhaps the gate needs to be taken out in one huge explosion (like putting out an oil well fire). Perhaps a 100 point warhead (or even more) You would have to design gate-buster missiles and would need a launcher big enough to launch them.
Steve
Throwing out more ideas:
A thought is that a damaged gate can still receive but cannot send.
Another is that a damaged gate has a percentage chance of malfunction. That would dissuade people from intentionally damaging their gates. Also, they could have a certain rate of self repair, so even if intentionally damaged, they would soon repair the damage. I can't think of a real good excuse why someone could build a gate but then not have an off switch for the self repair mechanism though.
I was also thinking that instead of being assembled by special ships, that gate construction ships are purely robotic and become the gate and therefore are one use machines. Once on station they reconfigure and lock in place. Say their engines are rebuilt in to the gate mechanism, or are consumed creating the wormhole, or whatever techno-babble sounds best for why they can't be moved once emplaced .
Yet another wild idea is that all warp points already have ancient indestructible gates of mysterious origin. Instead of a special ship being needed to build gates, a special ship is needed to reactivate a dormant gate (sort of a gate jump starter). Although it is pretty hard to make anything believably "indestructible". Perhaps they are massive, say the size of a medium size moon. But then they would be obvious and easily found eliminating the need for surveying, unless the survey is still needed to determine a precise course that must be set to transit the gate. I guess you could say they are cloaked by inscrutable alien technology and very hard to detect.
All in all though it is a pretty big stretch to come up with a believable reason why a physical gate couldn't be rigged with a command detonated antimatter bomb. Personally I would just make jump drives small enough to fit on warships so the military is not reliant on jump gates to carry on an offensive. You could make them expensive enough that it would not be economical to put them on freighters.