Hell no.
The collateral damage to the city and its citizens alone is enough to render his action unjustifiable. But even if all of the debris had been vaporized and the only people who died where the ones in the Chantry, it'd still be unjustifiable.
I understand wanting to destroy the symbol of mage oppression. But the vast majority of the people in the Chantry were not responsible for that. The few Mothers and one Grand Cleric that actually died in the explosion were vastly outnumbered by sisters and brothers and lay people, along with normal citizens who just happened to be in the building.
I wonder why Justice couldn't see the injustice that Anders's action would bring upon his victims. Maybe he had completely devolved into a rage demon by that point.