Bad design, good idea
This point has probably been touched upon, but I would like to throw in my 2 cents. The behemoth was an idea that was came to fruition lacking the potential of the original idea. Such a weapon would have the capability to end the was instantly, and would have be re-usable in the future (it's sheer size would have allowed it to be easily upgradable as new anti-fighter/anti-capship weaponry became available. It would act as an effective deterrant to aggression from other alien races for the foreseeable future. Would the nephilim really attacked a race when they have a large carrier group will the ability to erase their planet from space? Perhaps not. The behemoth would have a much greater psychological fear factor than a whole ship full of temblor bombs. Gigantic ships are always more scary than missles. The problem with the behemoth was that despite its size, it did not have the astonishing array of turrets and anti-matter cannons that it easily could have. It should have been designed to be bristling with guns, and they should have been up-and-running long before the superlaser was operational (as I am aware that at the time of it's destruction it was incomplete) The behemoth obviously had a formidable power supply for it's superlaser, and much like the concordia's phase-transit, the anti-fighter array should be able to operate even while charging the cannon. The power needed to power turrets and such would have almost certainly been an insiginificant drain on the supply. The danger approaching aship of that size should have been exponentially greater that even a concordia-sized dreadnaught. I can not see the kilrathi constructing a ship that big and not loading it with emplacements. Even just equiping it with anti-matter guns, with as light a loadout as one array of eight guns on each of the four sides of the ship would have made an approach by anything smaller than a destroyer a sure-fire way to get vaporized. The blast radius of eight anti-matter cannons would be large enough to scratch any bombers or convettes before they could get within torpedo range. And that's just without the benefit of any laser turrets. Good idea, very bad actual application of that idea. You'd think that at least one of the confed engineers would have seen the first star wars movie.