Then why take the risk of the Enterprise using the transphasic torpedoes at all?
If Starfleet really is expecting a massive attack, why not wait and churn them out to use on the Borg fleet all at once.
And risk losing half the Federation in the process? Since they know that it will take a longer period of time than the "one or two shots at most" of most traditional weaponry, it makes sense to deploy it in some small way to try and save what they can. The question then becomes whether to deploy it everywhere and try to stop everything that comes in, saving more worlds in the short term, but potentially losing the advantage in the long term when the next wave/full-on invasion comes.
So is what you're saying that the Federation should cut its losses and fall back to the core worlds (Earth, Vulcan, Andor, Tellar, and maybe one or two others) and hold out until the Borg arrive en masse, and do as much damage as they can before these worlds too are wiped out?
It seems to me that you'd want to put out what small fires you can, even using stopgap measures, in order to stall for enough time to devise some way of stopping the inferno.
All that said, if I were in Starfleet Command, I'd have given the torpedoes to at least a handful of other ships -- the Enterprise can't be everywhere at once.