That's true, although I guess the Alliance was kind of running against time there
- Gaius had given them an ultimatum and the three nations were so sure the Scions had been wiped out (including the player) and hence were a second away from throwing down their arms at Gaius's feet when the player showed up with Cid, Minfilia and Alphinaud, and hence were convinced to resist. Then, defeat didn't seem quite so remote, to the point they decided the best chance of survival was to launch a preemptive attack on the XIVth Legion.
Time really was of the essence - half the reason Operation Archon succeeded was probably due to taking the Empire completely off guard before Gaius could adequately organize his forces (remember, Gaius's arrogance kind of proved to be his undoing here - he was so sure the Ultima Weapon was invincible and could take anything the 'primitive savages' of Eorzea could throw at it, to say nothing of his conventional forces like his ground troops and magitek weaponry). Running around trying to find hypothetical weaknesses in Ultima Weapon which might not have even existed would have just wasted valuable time. They had to seize the moment and they did.