They screwed the pooch on the writing on these episodes. They're still good, they just just flipped things. If the crew had been busting ass to get what Jellico wanted done, not whining, and Jellico had made unreasonable--even outlandish--demands, we'd sided witht he crew. Instead, we have a captain trying to get ready for a war and a crew mad cause they've gotta put in a little extra effort.
I don't think the writers were trying to get the audience on the crew's side. They obviously wanted us to see both sides making mistakes. Funnily enough, Jellico turned out be the person that got a lot of support from the audience.