Pretty much, otherwise they're cowards willing to surrender over $600K to Mordor rather than fight for what's right.
A company that employs people has to tread lightly. The correct action of a company is to settle - unless each and every employee volunteers to risk their job and their paycheck in an unfair fight with the government. It would be unwise anyway to fight an opponent on a battlefield that the opponent selected, at the time of opponent's choosing. A $600K will look very attractive after a judge hits them with a $60M fine. Company's management is there to avoid that unfortunate situation. It does not even matter if there was or there wasn't any wrongdoing on company's part - not any more than medical help to injured motorists depends on who was at fault.
If the Obama's regime stays in power for another 4 (?) years then one possible response would be to move the entire company abroad, with every single employee relocated. There are many countries in the world (nearly all of them) that have better business climate; life there will cost less, so in the end the employees will be richer.