Three issues here ...
Firstly, could it happen? Yes, it could, because JMS does not own Babylon 5, Warner Brothers do and whilst, as I understand it, JMS and WB Have a gentlemen's agreement that they wouldn't do more B5 without involving him in some capacity, in strictly legal terms they could do exactly that if they wanted to. The only exception would be a movie, as JMS does retain those rights so they couldn't do that without him.
Secondly, should it happen? I agree that it shouldn't, because of all the reasons others have outlined here ... however ...
Thirdly, I think the question you are asking is not whether JMS would accept a script for a new B5 show from another writer, but whether JMS would accept another writer having creative control over a new B5 show ... a la Rick Berman. After all, there were plenty of scripts in seasons 1 and 2 of the original show that were written by other writers in line with JMS' outlines and vision for the show.
I have no problem whatsoever with other writers playing in JMS' universe, as long as JMS is overseeing them. a new show with a new Exec Producer/showrunner would be more of an issue.