Heck, in The Dark Knight Harvey Dent/Two Face is killed in just that sort of situation. To Gordon and any reasonable person it was a justified killing. It was just covered up to save Dent's reputation.
Now, in Begins the killing of Ras isn't as justified as it was pretty much murder by negligence or failure to act (sort of something like a "Good Samaritan Law.") At the point Ras was killed he wasn't a threat and Batman could have saved him and delivered him to Gordon/the authorities.
But the killing of Dent was certainly a justifiable act.