Josan said:
I've heard about this a few times and always thought it a lousy idea. The versions I've heard though never involved the Klingons. It involved the Enterprise crew preventing the assassination. And that made no dramatic sense at all. I seem to recall Nimoy commenting on that but could be wrong.
Either way, I think the studio did the right thing in keeping Gene away from the movies. I don't think he was a good writer. He certainly wasn't the best on the series.
As far as I can tell, the first reports of Kirk and crew saving JFK come from Shat's 1991 Memories, and Justman and Solow repeated his version in their book although none of them read the scripts. Only Paramount top brass and his assistant Sackett read the drafts. According to Sackett, every draft involved the Klingons stopping the death of JFK while Kirk and Spock had to fix the timeline.
There are also quotes from Shatner where he says the opposite of what he wrote in his book, claiming that the cinematic climax involved Spock on the grassy knoll.
Mike Okuda, according to other posters here, also read it and commented on it.
Considering that, of all the published comments about the script, only Sackett actually read it, I trust her version more, especially because it follows the City/Ellison format more closely.
Still, it's a mystery.