What went wrong was at the center of the first congressional hearing Thursday into the botched rollout, with contractors on the project blaming the Centers for Medicare & Medicaid Services (CMS)—a division of the Department of Health and Human Services. CMS was in charge of pulling together the work of many contractors for the Oct 1. launch.
"Assigning this to CMS, which doesn't have experience integrating these complex IT systems, doesn't have experience in e-commerce website development, was not a wise choice. I didn't make that choice," said Emanuel.
A CMS spokeswoman acknowledged the issues raised by the contractors—saying "due to a compressed time frame the system wasn't tested enough," but that's changing now.
(Read more: Obamacare contractor promises: We'll fix it soon)
Gottlieb, who served as an adviser to CMS during the George W. Bush administration, said: "The reality is they will get these IT issues sorted out. I think the risk is that the entire market in 2015 gets repriced off the experience in 2014."
Emanuel responded: "That's something that Scott and I agree on. If it's a very difficult market within the next five week … it could rebound in 2015."
"These are technical problems that are blocking and tackling, and that will be solved," he said. "Over the next year, it's going to be a much better shopping experience. Then we're all going to look back and say, 'Wow, this was a great restructuring of the health care system."
Gottlieb disagreed: "I think people are going to be surprised by the very limited choice they have. And the difficulty is once you go outside your network in these plans you're going to be faced with very high co-insurance."
Emanuel said the insurance companies learned from the managed-care backlash of the 1990s and they're going to put measures in place to protect against that. He said he has advocated that people who get serious illnesses such as cancer be allowed to get a second opinion out of network for in network costs.
—By CNBC's Matthew J. Belvedere. Follow him on Twitter
. Reuters contributed to this story.