It’s no secret that Paramount has all but decided not to pay the Kirk family for the Kelvin Star Trek franchise, but that doesn’t mean they can’t still move forward.
Before getting into the subject at hand, I want to point out that the truth of the matter is that Paramount should be paying Chris Pine in line with the amount he is entitled to for being the lead character in a major franchise revival. Star Trek Beyond made a profit, as did the two previous entries, the studios wish to bring in more profit by cutting payroll shouldn’t be his concern, it’s theirs alone. The irony of course being that the studio is looking to cut the budget and tell more personal, and more ‘Star Trek’ stories, the exact opposite of the approach they started with in 2009.
Assuming they’re going to stay on this course and move forward in a Kirk free galaxy, recasting him wouldn’t be distasteful because of a new actor in the role however it would be distasteful in that it was for budget reasons, they have a few built-in stories that would allow it to be easily accomplished.
The fate of Kirk…
Captain Kirk made no secret of his dislike of the episodic nature of his recent travels on the Enterprise during Star Trek Beyond in fact he spent most of the film contemplating telling his crew that he was ready to take a starbase job, obviously we know the character is incapable of sitting behind a desk filing reports for the rest of his life.
"Let me tell you something. Don’t. Don’t let them promote you. Don’t let them transfer you. Don’t let them do anything that takes you off the bridge of that ship. Because while you’re there, you can make a difference.James T. Kirk"
Since the Kelvin Timeline Kirk hasn’t yet learned this lesson it would be perfectly believable for him to take the promotion, if only to go right back after the Enterprise a few years later as he did in Star Trek The Motion Picture.
Spock in command, Kirk off-screen.
We know Spock is the next in line for Command of Enterprise, at one point he was even ahead of Kirk in line for the Enterprise, so we could carry on with Captain Spock in command, maybe even with a young Commander Will Decker taking the first officer’s chair.
This would be the least disruptive way forward, Kirk would still be mentioned and act as an off-screen character for the movies, leaving the door open for a return down the road, or maybe even a spin-off action adventure where during an ill-fated experiment aboard the station the Kirk’s are displaced in time and we get the James and George buddy movie we’ve been hearing about for years.
Separating the crew
The more aggressive version of the path forward is to go right ahead and separate the crew, Sulu becomes Captain of the Excelsior, perhaps one or two faces go with him, Spock moves on to his role as Fleet Captain, running the Enterprise as a training ship, and McCoy is reluctantly forced out to some front line medical disaster on the edge of Federation Space.
Eventually they’re all reunited, as they solve the story-worthy problem that faced them shortly after the movie began, allowing us a chance for Scotty to grumble about the supposed Transwarp capabilities of the Excelsior, and McCoy to be terrified of getting beamed back to the ship.
This path leaves many possibilities open for the writers, it even allows for the growth of spin-offs ranging from Starfleet Academy, to the Excelsior Chronicles, to the Kirk time travel buddy pic.
Alternately they could just go right on to the Kelvin Star Trek The Next Generation that would also be acceptable.