Is Obama's JAMA paper OK?
Authorship: This one is messy. The JAMA instructions say Authorship credit should be based only on (1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; and (2) drafting the article or revising it critically for important intellectual content; and (3) final approval of the version to be published based on the acknowledgements, I think there is a case that Matthew Fiedler, PhD, and Jeanne Lambrew, PhD could be authors for their contributions to planning, writing, and data analysis while those who only edited the manuscript fail the test.
The difficulty is that the JAMA requires written permission from everyone named in the acknowledgements. For whatever reason, the contributors did not feel they deserved authorship. It is possible that they were bullied out of authorship. Universities, and I am hoping the White House, have systems in place to handle this type of bullying. In the absence of any evidence wrongdoing, I think we need to assume that credit was fairly given.

Political papers: This is also a little messy. I think good scholarly journals should include non-research papers (as long as they are clearly mark something like special communications) that likely have broad appeal to the readership. I think journals should strive to keep readers up to date on important issues in the field, even if it is not original research. I also think journals should actively engage in activities that will bring wider attention to their respective field. I think the specific paper falls well within the scope of JAMA which includes all subjects that relate to the practice of medicine and the betterment of public health worldwide. What makes things messy is that in addition to Special Communications JAMA also publishes Controversies in a point-counterpoint and Health Law and Ethics, both of which may have been better fits. Given the partisanship surrounding obmacare a Controversies may have been a fairer way to present the issues.

Conflicts of interest: The JAMA instructions say A conflict of interest may exist when an author (or the author's institution or employer) has financial or personal relationships that could inappropriately influence (or bias) the author's decisions, work, or manuscript. and I don't think that being the originator of an idea counts as a personal relationship that would qualify as a conflict of interest.