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 Countdown part is not freaking likely since Countdown wasn't even a twinkle in Dan Didio's eye when Id.C. was being written. The part about Brad Meltzer not knowing who the hell the true criminal was until the end, DOES seem to fit very, almost uncomfortably, well.
- More likely, they did know who the true criminal was, but it was originally planned to be someone else...
The original choice for the true killer was...
- Someone planning to put Dr. Light back in business
- Superboy Prime (or perhaps Kal-L)
- Heat vision of the silver age variety might not leave trace evidence, and silver age super-speed was certainly capable of Flash-like vibration through solid matter. Silver Age Superman once even traveled to the future that way.
- Mr. Mxyzptlk from Whatever Happened to the Man of Tomorrow continuity. Somehow Crisis on Infinite Earths brought him back to life and allowed him to sneak into the single Earth created. He has been slowing picking apart this universe by causing events that do not have rational causes or outcomes. His plans nearly came to fruition with Final Crisis but the superheroes just barely managed to stop him. For now.
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!
- Maybe it was a modified gadget of the Atom. That's probably how Jean easily shrunk it down to being along with.
- It was the Scarlet Witch saying, "No more trace evidence..."
The fight with Deathstroke went differently, the version we see is the one the superheroes have agreed to tell because the truth is too embarrassing
When 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.