They could be fined hundreds of thousands daily for refusing to act. We recently found out this happened to Yahoo in 2008 [1] via the FISA court. Apple shareholders wouldn't like that.
I'm pretty sure Tim Cook and his lawyer mean it when they say they will comply with the law. Apple engineers need not worry so much about quitting their jobs over this. If I were there I would stick with Tim Cook. Consider,
If Apple loses this case, this becomes a gigantic public debate where we scramble to enact legislation that removes this power from the government.
If Apple wins this case, and the government pursues anti-encryption laws, this becomes a gigantic public debate.
If the case is delayed for 2 years and goes to the supreme court, this becomes a gigantic public debate.
Regardless, since this is in the public sphere, whether-or-not-we-put-back-doors-in-phones is going to become a gigantic public debate.
The only way it doesn't become a big debate is if Obama comes out and says he's been informed on the issue and now realizes encryption in our phones is, on balance, a good thing.
[1] http://www.theguardian.com/world/2014/sep/11/yahoo-nsa-lawsu...