I hate that aspect of B89 and Returns, and both movies were rightly criticized for it.
As for the TDK trilogy, none of them portrayed Batman as a merciless killer. Any people that died by his hand were in an attempt to save lives (Harvey trying to kill Gordon's kid, Talia about to nuke all of Gotham). Ra's was not his fault. He didn't put Ra's on the train, and he didn't smash the brakes. Not to mention the movies even made a point to criticize when Batman got reckless, like when Alfred chewed his ass out for the Cop car chase in Begins.
As for the early comics, they ended that portrayal of Batman because of fan complaints of seeing him kill people. The most controversial one was when he used a gun to shoot down some thugs. It was a fleeting controversial and unpopular interpretation that lasted a year or so, and flies in the face of over 70 years worth of characterization of who Batman is.