Just like any military decision, the bombing of Kilrah is a tactical and a moral one. When I first saw the solution to the Kilrathi war in WC3, the first thing I thought about was the bombing of hiroshima and nagasaki during WWII (the second thing I thought of while I was on the mission was the Death star proton torpedo run in Star Wars - Right actor, wrong universe). True the situations are slightly different, but the military decision is the same. Do you sacrifice another culture's civilian/military lives to save the lives of your own people?
The answer is going to be yes everytime.
In WWII the justification was that we were saving countless American lives and that, in addition, the only way the honor-obsessed Japanese were going to surrender were with a total and undeniable defeat.
In WC the justification was to save countless Confed lives (in the inevitable Kilrathi victory) and that, in addition, the only way the honor-obsessed Kilrathi were going to surrender were with a total and undeniable defeat. Sound familiar? (oh and by the way, I'm not comparing our asian friends to the blood-thirsty Kilrathi, just the situation).
It's just a judgement call by the military leaders in charge when they have "the biggest gun in the galaxy" (quoting pre-insanity Tolwyn-well maybe just a little insanity).
The greater good must be served . . .(notice how the greater good is usually the worst imaginable decision for the losing side)
In the end, the best decision was to use the T-Bomb, whether it was right or not, that's for philosophers, not combat pilots fighting a war.