Sure, but at that point Apple could be held liable for knowingly selling the app (and why you assume Jobs is personally handling this, I have no idea). This is the way almost every content company works: when they receive a takedown notice, they comply. Whatever money Apple is making from the sales of the app pales in comparison to the amount of money the Times' lawyers could wring out of them. If this kind of thing became a problem that was significantly affecting the platform, they may need to step in, but for one-off cases they're not going to.

They're a publicly-traded business; they don't run on fairy dust and unicorn tears.