By your definition Rosa Parks wasn't performing a legitimate act.
There IS a real second legitimate choice---get the legislature to pass a law overruling the court.
The law that the Catholic Charities is supposedly violating was very clear in its exemptions--and the court simply redefined what a religious organization is so they could save some woman from the horrific slavery of paying for her own birth control pills. If they pass another law, what should it say, "We hereby declare that religious organizations don't have to provide birth control, and we really, really mean it this time"?
When a bunch of black-robed idiots tell us that free exercise means the government tells you how you will serve your God, civil disobedience is more than justified. Don't get me wrong, they should let the appeals play out, but if the SCOTUS comes down with a ruling supporting the State's double violation of the 1st Amendment, the Catholic Charities should say, "Go ahead, make me."
Got it in one!
Nothing wrong with "civil disobedience" as long as one is will to PAY THE LEGAL CONSEQUENCES, until the law is changed.