Killing Joke didn't start out as supposedly being in-continuity, so it got an early pass on some of that.
As for "the rape" revealed in Identity Crisis, that was just adding insult to injury with who was killed and why.
(As for all the deaths, Crisis on Infinite Earths at least seemed to have some shred of dignity in those deaths, as opposed to things like gutting Phantom Lady and knocking Pantha's head off and having it go flying away in Infinite Crisis.)