That's fine for ground combat ... how does that apply to aerial bombardment? You don't just loiter up there, waiting for the enemy to start shooting. So ... You need prior intelligence, telling where the enemy is storing assets, or where their troops are hanging out.
you do what you can, if possible to protect them, however, not at the expense of your own troops or civilians.
So you don't level an entire city block to destroy one building. That would indeed be "disproportionate", in the Just War sense of the word.
(I think we're in agreement here.)
I would say you do what you can with the assets and intelligence you have. If your assets (weaponry) are limited to something that would destroy a block to take out an enemy building, you may have no choice. If you have 'smart bombs', it may be in your best interest to use that, not just for limiting collateral damage, but because you may need to utilize the infrastructure if/when you move in as a ground force. Those decisions should be left to military commanders in field or whom have the correct intel and information to make that decision, not to arm-chair philosophers.