Apple has most certainly taken a moral stance in the past as you point out. The galling part of the article to me was "The company has not fully tested its political and economic leverage in China." It is not Apple's job to take a political stance. They can if they want, as evidenced by the examples you laid out, but there is no requirement. If the NYT wants to talk politics and precedence, perhaps they should direct their criticisms toward the U. S. government, et. al., who collectively think that China's membership in the WTO, and therefore I assume free trade with China, is just a-okay.

Apple is playing by the rules, and this time decided that this is not the hill they want to die on. That's their prerogative. Don't like the rules? Then go complain to those that make the rules to begin with, not those that play by those rules.