The Law of Armed Conflict (LOAC) that governs wars on the international sphere allows you to bomb a house with enemy combatants (and civilians) in it who refuse to surrender. EU law does not which is why British troops have been for several years been hounded by EU lawyers.
There was a lot of consternation in the US military last decade that it was under media pressure forcing them to go well beyond what it had to do under the LOAC and they would have been right they were going beyond the Geneva convention in many of their urban combat battles, but COIN operations or fighting terrorists are as much political affairs as anything else so one can't completely ignore the political/media side. I will say when fighting ISIS in Mosul the gloves did come off and the rules of engagement were closer to Vietnam or Korea levels. Iraqi, French and American rockets were pounding the city and air power was helping the ISF overcome enemy entrenched in buildings. In WW2 or ACW we would have burned the city down with incendiaries before any troops were sent in.
Is it acceptable in war under the Law of Armed Conflicts today to bomb a military facility with thousands of contractors? Yes. But, there are political implications to whatever you do when at war or in this case undeclared war.