They were not able to evaluate how massive the attack was.
They probably did not have much forces available anyway.
It also seems they needed some help from other countries/forces, which takes time.

They did not want to bombard at first, because of the collateral that remains high even when you try to evacuate the region. There's also the fact you ruin such a city that Kyoto is.
But at some point, it was that or totally losing the region.

They probably could have bombarded an hour before, but many soldiers would have died with the BETAs. The city would have suffered minimal damage though.
But the choice was similar to the one presented to Yui. They were not able to do it at first, but were forced to in the end.