True, but the question of whether private companies are permitted (legally or morally) to engage in blatant censorship is a critical question that needs to be answered sooner rather than later. The moral standards of super-mega-fundamentalists are already applied to mobile appstores, e.g. Apple pulled the mobile version of one of the biggest German print publications because they didn't like German law&morality and decided they have a right to tell people what they are allowed to read/see, and what they aren't. This is as unacceptable as it would've been if B&N had done what they were accused of.
Though you are of course right to point out that B&N has apparently not actually done this - nevertheless, it's still not a "nothing to see, move along" thing. This kinda stuff does happens routinely, maybe not by B&N, but Google&Apple certainly do it as SOP.