I very seldom encounter books that are cheaper to buy (new) physically than electronically. I agree that the electronic versions should be even cheaper, but that's a separate story. The first order reason that ebook prices rose in response to Apple's entry into the market is simple -- competition. In this case, Amazon had a monopsony and dictated prices to publishers. Apple broke or offered the whiff of a break in the monopsony and the rest is history. What does this competition look like up close? A bunch of contract negotiations.
Did Apple "orchestrate a conspiracy" to raise ebook prices? That's another question altogether. The video of Jobs saying prices won't be higher simply indicates he knew about the "most favored nation" contracts. I couldn't be bothered reading through the entire judgment, but certainly followed coverage pretty closely and I just don't see a case.