For one thing, I think Jackson would have talked Lee out of Pickett’s Charge on day three of Gettysburg, assuming that there had been a day three. Jackson didn’t like set-piece battles, which is why he was both an effective commander and one of the modern military thinkers of that era. So, I don’t believe there would have been a three day battle in that one location.
Jackson fought under Lee for about a year through some of the fiercest battles of the war and I'm not aware of a single time he questioned Lee's orders or tried to talk him out of any strategy. I doubt that Jackson would have started doing so at Gettysburg.