The opposition should be between "malicious terrorist acts" and proportionate, maximally controlled acts of self-defense.

The occurrence of innocent civilian deaths on enemy territory is justifiable when you are defending yourself, and when you are doing everything possible to minimize if not eliminate the possibility of such civilian deaths in rooting out the source of the aggression.

Thus, Bolton is right in that a priori it's not "the same act to deliberately target innocent civilians" and to cause the deaths of innocent civilians in the course of self-defense, if all is being done to minimize those deaths and no alternative is left.

Truth unfolds in time through a communal process.