Whether or not Riker was correct is absolutely the issue. He deferred to his captain without question in the Pegasus and it haunted him for the rest of his life. Picard specifically wanted him on the Enterprise when he heard that he'd disobeyed the captain's orders when they went against his better judgement. And Riker was also correct to point out that part of his job as XO is to speak up when the captain is wrong. He did the same when Picard had been replaced in an experiment.

As for insubordination, if they don't have time to talk about what schedule makes the most sense, they shouldn't have time for a trial. Jellico didn't know how to lead, and then blamed Riker for not knowing how to follow.