You know, I stopped reading Identity Crisis after an issue or two: I was just so repelled by the way in which the writer was treating the characters. However, mw, in his typical clear-headed way, explains the story's merits as a mystery, which prompted a thought. 

To employ characters with well established patterns of behavior and consistently displayed character traits in the service of said mystery was what was unacceptable. Maybe I would have been more likely to stick with IC if it had been written as a Watchmen-styled alternate universe allegory, in which, say, the fear that Batman has fascistic tendencies or in which a criminal might well indeed rape a hero's wife to seek revenge would have been believable. 

Because I didn't stay with it, I can't speak authoritatively, but I'm guessing DC was trying to set up some changes in whichever universe IC was supposed to have occurred: therefore the use of the icons of the company. And I'm sure they didn't want an Elseworlds- or Watchmen-style story b/c they wanted to show the grim, gritty, dark, (choose your tired adjective) side of characters the suits in charge regard as too chivalrous, noble, etc., etc.