In all likelihood, Time Magazine protected him by not reporting fully and accurately to DHS on the cause of his termination of employment.
For all we know, Times protecting him from the DHS inquiry may have been in exchange for leaked information at any time in the future, should the Times request it of him, or should he come across anything that the Times would want.
Or, it is equally likely that the DHS background check was lacking in diligence, which won't come as much of a surprise if that is the case. Companies queried in background checks should be profiled for their "loyalty". The less loyal a company, the more rigorous the background checks of employees leaving such companies for Federal employment. This will work well for people who are being blackballed by their former employers, as the inquiry would uncover such, and it would severely penalize any company which withholds information relevant to a DHS security inquiry regarding an application for employment with a Federal organization.
It should be illegal for a company to not disclose all information regarding a person's employment, when that person has applied for work requiring a security clearance. Isn't part of the security clearance application a waiver for just such an inquiry? If so, then the company in question has no reason to conceal negative information.
Yet another thing for which to thank the filthy greedy pond scum of the Bar.
-ccm