People are reading too much passive aggressive intent in Riker's behavior I think. Riker is trying to adjust to a captain with a radically different command style. This takes time. Jellico is expecting Riker to read his mind practically..
I think it was the exact opposite actually. No mind reading necessarry. Jellico was very deliberate in his instructions to each department but often received kick back. As a new Captain with a short window to make preparations, that would have been extremely frustrating to Jellico. He may have had his flaws but if he was good at anything it was making his instructions crystal clear.
You say you don't like the sheep mentality but you should only be calling your CO out if he is providing unlawful orders or behaving in an inappropriate manner. Jellico asked for difficult changes to the crews respective departments but there was nothing there that deserved an uprising. The senior staff should have been communicating their concernes upwards through the chain of command, which most of hem did. The problem was that Riker didn't do a great job in serving as that conduit. I say again that voicing your concerns and backing up your department is fine but when the decision is made by the Capt then your job as an XO is to live up to the title of the position; "execute."