The branding being new has no bearing on whether killing is new.
When Batman shoots people in TDKR it's specified to be with rubber bullets, and he doesn't bomb people. He makes a big impassioned speech speech about how bad guns are, and one of the central conflicts is his desire to finally break his 'one rule.' He's brutal, but he doesn't kill anyone.
And even if it were definitively proven that Batman only started killing recently in the film, which it hasn't been, it still doesn't change the fact that the central conflict and the Martha moment would have been far more powerful and just plain better if Superman was the only person he ever considered killing in the movie.