What the difference between his version and what they did?
The general plot was the same, but the stories were very different.
In Ellison's version, instead of McCoy going back in time and changing history, it was a random crewman who had been caught dealing drugs on the Enterprise and was being taken down to the planet to be executed by a firing squad. The Guardians of Forever were 9 foot tall aliens rather than a single round portal. Also, Spock was the one who let Edith Keeler die, because Kirk couldn't bring himself to sacrifice her.
IMHO, every change that was made to Ellison's original version improved the story.
“What the difference between his version and what they did?”
Basically, millions of dollars in today’s money. Ellison was a Sci-Fi writer not fettered with TV budget and time constraints. Supposedly, Roddenbery and another writer locked themselves in a room for days with nothing but cigarettes and booze in order to “fix” it.