Your point is good - that's a isolated event - but it was a isolated event that was taken into account in the military actions that followed.
And yes. If the soviet union had destroyed munich and frankfurt (Frankfurt was the transportation hub of the western front) to force Hitler to surrender it would have been justified. To draw the full conclusion - it would not have been justified to bomb Geneva (since it wasn't a military target).
And frankly, bombing Frankfurt would have been far far less heinous then what the Red Army did to East Prussia, which could not be justified. The difference there is that the soviets had already overrun Prussia when they committed their war atrocities. Likewise, what US solders did to German PoW in more isolated circumstances.
About the bombings, the targeted bombing wasn't working very well because of weather, so they decided to obliterate cities with incendiary bombs, civilians and all.
But returning to mass murdering civilians to advance military objectives: what would you think of the Soviet Union destroying with atomic weapons Munich and Frankfurt, to force Hitler to an unconditional surrender? Would reducing the deaths of soviet soldiers be a good justification?