I was thinking in terms of having a HTK of e.g. 1000 (or even 10,000 or 100,000), and treating them as "all or nothing golden BB" the way SY are, i.e. any particular hit would have a chance of strength/HTK of completely destroying the gate. With this destruction mechanism, you'd pretty much have to:
A) Rig a bunch of 100pt bombs (all-warhead missiles) to the gate in advance, and blow them all at once in the hope that one of them blows the gate.
B) Have bunch (or maybe just a single, if you've got enough time) beam-armed ships sitting next to the gate, ready to start blasting away if things get dicey.
C) Burn through the magazines of several (or more) missile ships shooting at the gate.
I really like B, because it gives another raison d'etre for beam-armed ships, with A as an alternate method for pure-missile races.
As for technobable, I like the idea that a jumpgate isn't actually a physical object - instead it's a stable wormhole which the weapons fire has a (small) chance of disrupting. With this technobabble, only energy weapons and explosions would have a chance of destroying the gate - gauss cannon and railgun shouldn't (the slugs would go right through).
One of the things I like about requiring weapons fire from the far (enemy) side is that it gives the enemy an opportunity to interfere with blowing the gate, which gives more of an opportunity for "last stand" situations to show up. Having civilian ships deconstruct them from the near side in a predictable amount of time seems a lot less exciting - although my ideas on this might change the first time the enemy launches an assault through the gate while the construction ship is trying to deconstruct it. Hmmm - the far-side weapons-fire method also acts as a counter to the energy-combatant "duck through the wormhole when the missiles are due to arrive" strategy against missile ships - ducking through the gate means you can't be working on destroying it, so there's motivation to try and tough out the salvo rather than dodging it for longer than the missile loiter time.
I was going to say that I liked the idea of the disruption blowing the gate in both directions, and was almost ready to suggest "why do I need to build a jump gate on each side?", but then realized that this would allow deconstruction from the near/safe side which (as described above) I think is a lot less interesting.
John