The funny thing to me is that Baker thinks he's making a new point. He's clearly never watched "The World at War" (made in the early 80s IIRC) which spelled out in great detail how all sides suffered in the war. He's also plainly unaware that the morally dubious strategy of bombing German cities is why Bomber Command never received the public recognition of campaign medals, unlike every other aerial, naval and ground action.
He's also starting from a premise which is provably incorrect. The question "is this a morally justified war?" is asking whether the reasons for going to war were morally valid. But Baker starts from this question and then answers a completely different question: "were the methods used to fight this war morally justified?"
The answer to this second question is clearly "no" in the case of firebombing cities, because even though the military targets of factories and railways were destroyed there was also a dreadful toll of civilian casualties. But the answer to the first question is equally clearly "yes" - attempts at appeasement throughout the 30s had only led to further annexing of central Europe, despite German assurances each time that they wouldn't go any further, and it was clear then and now that without intervention the Germans would only stop when they controlled the whole of Europe.
This is a classic politician's trick - when asked one question, answer a different one. Most people dislike politicians who won't give a straight answer to a question. I see no reason to think otherwise about authors who do the same.