The ending of Identity Crisis wasn't decided until sometime during the writing of the second-to-last issue.The outcome of the story makes no sense given the facts established earlier on. The flamethrower comes to mind. The surprise twist at the end was most likely mandated by the editors for some nefarious purpose, possibly to set up Countdown.
The original choice for the true killer was...
That wasn't a flamethrower that Jean was packing......It was a fire blower which shot fire from the fire dimension! Because real flamethrowers use a petrol compound to burn, and there would have been trace evidence. This is the only way to explain why the Cabal could have possibly thought that Dr. Light was the true killer since a flamethrower absolutely does not fit Light's MO. ...Well that or Brad Meltzer is a bad fucking writer, BUT STILL! And I swear to God, NO FREAKING SUPERBOY-PRIME PUNCH JOKES; IT'S GOTTEN OLD!
The fight with Deathstroke went differently, the version we see is the one the superheroes have agreed to tell because the truth is too embarrassingWhen they saw Deathstroke willing to fight a lineup of the Justice League they doubled down in laughter, and Deathstroke, not being an idiot, bashed them on their heads until Green Arrow punched him in the balls. After that they agreed to the story and altered Deathstroke's memory to fit it.