It's been years since I read Ellison's version, but...
Star Trek was pitched as both "Wagon Train to the stars" and "Hornblower in space". These concepts remained in even the final version of the show's writer's guide.
The first concept allowed for "lower decks" stories where the starring cast had little involvement. As the show developed, however, the success of the Kirk/Spock/McCoy dynamic, Shatner's ego, Nimoy's popularity, and other factors made those stories unlikely. Still, the style of the show was quite fluid early on, and the potential for a kind of anthology show with recurring characters was there.
The second concept was based on the idea that communication with Starfleet Command was often impossible without huge delays, making the Captain essentially autonomous. This idea was virtually ignored almost from the start, with communication happening at whatever speed the plot demanded, instantaneous two-way conversations (or the appearance of same) occurring frequently, and much downplaying of the huge expenditure of resources needed to increase transmission speed.
Ellison began writing in March 1966, long before the series was on the air, and submitted his final re-write that December. At that time only 12 episodes had been shown, and even if Ellison had access to ongoing production - which I doubt - the tight production turnaround at that point wouldn't have revealed much more about the direction of the series than just watching it on TV.
Given all this, I don't blame Ellison for wanting to help steer the development of the characters and the show, including Kirk handing out (final) frontier justice. Heck, if he was successful, Ellison could have become a staff writer. It would have been a different series, but it might have been a good one. Roddenberry and his team had other ideas. I think it's only because of Ellison's well-known crankiness that the feud ever happened.