The headlines sound dire, and the storyline is a bit confusing. So let's get right to the bottom line: this lawsuit by the Department of Justice accusing Apple of conspiring to fix ebook prices is no big deal for Apple. Ebooks are a tiny tiny portion of Apple's business. My impression is that even a worst-case-scenario regarding this suit would have a negligible effect on the company.
The DOJ actually sued five publishers in addition to Apple, and three of them have already settled, without admitting any guilt. Two of them, like Apple, have chosen to fight the suit.