This week, Congress cut off funding to the activist group, which had nearly $1 million embezzled by its founder's brother and has been accused of voter registration fraud.
As Obama's problems get bigger, columnist Noonan said she worries that government will also get bigger.
"I understand the anger," she said. "They're going to make it more expensive now," she said of fears about health care reform.
"And they're going to make it more intrusive in my life, forcing me to buy, say, insurance if I don't want to or a penalty if I don't," she said.
"Do I want that now, with the economy in the shape it's in and with being worried about my nephew, who's over in Afghanistan and is he coming back? No, I don't think that's where people are."
She said the president will likely win some sort of health-care reform. "There will be a headline that says 'Obama gets health insurance'-- or whatever he gets, however it's put -- but I think it will be a sort of victory that makes people think, 'That's not what we need.'"
But Robert Shrum, who was a senior adviser to Al Gore's 2000 presidential campaign, said Obama should continue to use what he called the "biggest megaphone" to push for change.
"He doesn't have any choice about what's on his plate," Shrum told ABCNews.com. "He understands that if he does not do health care in the first year alone, it won't be done at all.
"He has to do the economy and he has to do financial reform and he has to deal with foreign policy crises and the climate change imperative," said Shrum, who expects Obama to pass health care reform and get a fight over climate change next year.
He compared the current president to John F. Kennedy who got "almost every big decision right -- on the new economics and on civil rights and trade and the Cuban missile crisis."
"You don't pick these things," said Shrum. "Bill Clinton said his greatest regret was being president in quiet times."