Your explanation of Stuart makes a tremendous amount of sense. The "Gettysburg" version portrays him as being on the verge of insubordination. Never seemed to make the sense that goes with the Stuart and Lee personalities. But then again, folks have re-written this, that, and the other for the fame and glory of it all. This view probably raked in the bucks for the Gettysburg folks too.
All in all, my guess would also be because Jackson was no longer on the scene. One of the leaders was forever gone, and it just hadn't really sunk in to Lee's mind yet!
It only took Lee one battle to figure it out. Unfortunately, it was Gettysburg, but that is war. Jackson could not be replaced, and the Army of Northern Virginia suffered from his loss the rest of the war.
The only thing about movies is that they become accepted truth. It makes us lazy. When a historian goes back to the original sources and tries to correct the record, they are dismissed because (gasp) that's not the way it happened in the movie.
Stuart did the job he had always been expected to do. With the army in Northern territory, cut off from their own supply lines, they had to gather provisions by taking them from the Union army. Had he shown up at Lee's headquarters with 125 wagons loaded with supplies and munitions on June 30th instead of a few days later then his reception would have been a whole lot different. As someone else pointed out earlier, Lee had sufficient cavalry to scout the Union army. He just misused it.
All in all, my guess would also be because Jackson was no longer on the scene. One of the leaders was forever gone, and it just hadn't really sunk in to Lee's mind yet!
Had it only been the loss of Jackson the confederacy could have muddled on. But a campaign into enemy territory is a daunting enough challenge without adding an army reorganization (two corps into three), two new corps commanders (Hill and Ewell), half a dozen new division commanders, and a number of new brigade commanders, and so on, and so on. None of Ewells division commanders had worked for him before, and for the most part it was the same with Hill. With as many senior commanders as that new to their commands then confusion is to be expected. It was unfortunate timing.