It's been a few years since I read the WC3 novel, so my recollection is probably incomplete, but thinking back I can't understand why Confed HQ didn't put a higher priority on the Behemoth endeavour, given that they knew how badly the war was going.
Granted, Tolwyn had burnt some bridges and was maligned by elements of the command structure and the Behemoth was incomplete, untested and a very risky proposition. There was also the additional pressure compelling Confed to up the ante and respond to the Kilrathi bio-weapon attacks, which may have forced an already accelerated deployment of Behemoth. Given all of these setbacks, the Behemoth was still a viable solution to ending the war on favourable terms and with Paladin's Temblor Bomb project in limbo at the time (without Dr Severin), it was effectively the only solution.
Knowing that, I find it hard to realistically comprehend within the game universe why Confed HQ proceeded with half measures on the operation, when they knew that the Temblor bomb wasn't yet viable. During the operation covering the temblor bomb strike, a considerable Confed force was assembled and yet a paltry few ships was deemed adequate to cover the Behemoth.
Although I can't recall any specific timeframes for the Behemoth regarding time to charge the weapon and the required/optimum firing distance, the Kilrah briefing simulation would suggest it to be fairly quick, i.e. exit jump in Kilrah, charge weapon and fire; so perhaps a couple of hours at most? As you indicated Loaf, the Kilrathi obviously monitored fleet carrier movements in great detail, yet as evidenced in End Run, Confed have the ability to obfuscate large fleet movements to varying degrees and for limited periods, although the Kilrathi would undoubtedly realise something was up before too long, but not before a concentrated breakout could occur.
I would suggest that given the will and determination from HQ to put the highest priority on the Behemoth operation (surely the only viable solution at the time, game plot aside?) that the bulk of the fleet could be gathered around Behemoth for a push through to Kilrah. While losses may have been high, with that kind of protection, the Behemoth should have been able to make it to Kilrah and deploy, even if destroyed afterwards or on the return to the lines, while the remaining ships fought a rear-guard action to allow the fleet to return to Confed space. Assuming the Behemoth deployment was successful, a large portion of the Imperial fleet assembling above Kilrah would be destroyed as well putting Confed in a very favourable position if the Kilrathi continued the war.
While I recognise and accept the WC3 plot within the context of the game, which works well by increasing dramatic turns and ratcheting up the suspense, within the wc universe "reality" at the time, I fail to see how Confed HQ could do anything but fully support Tolwyn's Behemoth operation.
Cheers,
BrynS