No, the Catholic Church was not on board with Obamacare. Check the names of the links here.
http://www.freerepublic.com/focus/f-religion/3229924/posts?page=16#16
Their moral compass is so screwed up, they're incapable of recognizing that any mandate in healthcare is immoral. They don't oppose the requirement to provide mental health services, but there are religions that hold this is immoral. All they want is for their narrow religious view to have a special carve out.
That's all.
They consider contraception and abortion offensive to human dignity, without understanding that liberty is the strongest affirmation of human dignity there is, and that when they advocate for its denial, they're no better than the people they [temporarily] oppose.
Read this letter carefully, and tell me that you can honestly claim that the chief USCCB advocate for "human dignity" actually opposes 0bamacare. He doesn't: he supports it, as long as his own little ox isn't the animal being gored.