Even if JMS or Ron Moore had made the show from day one it would've been canceled. Moore's BSG is canceled after 4 seasons and until TNG intervened so was Babylon 5. Neither of those acheived the kinds of ratings UPN wanted, and the change in management who was against sci-fi programming would've ended it regardless.
If JMS had been in charge from the beginning, it wouldn't have lasted a season. After completing B5, TNT messed him around with Crusade. Joe's direction is pretty much you do it his way or you don't do it. Hence he forced them to pull the plug during the first season. He'd have been no different with UPN.
Straczynski also walked away from Jeremiah after its second season due to MGM's meddling, in effect forcing them to cancel it.
Ron Moore? Again, contract or no contract, it's unlikely that he would have stuck with the series with UPN looking over his shoulder. He was given a creative freehand by HBO for Carnivale, and Sci-Fi with nuBSG.
Bottom line, cancellation's not the end of the world if your vision's being screwed into something completely different. Straczynski's stood to that principle on more than one occasion. Moore's never had to. Berman and Braga, plodded on regardless.
I'm happy to take your word for it that they did the best that they could under the circumstances, but to be honest, when the writing's on the wall, which it was with Voyager, its audience shrinking with each passing season, they'd have been better served trying to rescue their reputations, and let someone else drive the franchise into the ground.