The NYT portrayed the Fed as facing a serious dilemma in dealing with its portfolio of mortgage backed securities (MBS). It argued that it can either start selling them now and risk slowing the economy or wait until the economy has recovered more and risk losing money by selling them in a higher inflation environment.
There actually is another option that would address the deficit concerns that appear constantly in the NYT and other media outlets. The Fed could simply hold the bonds indefinitely and then reinvest the proceeds in Treasury bonds when the MBS are paid off. This means that the Fed would have a constant flow of interest income which would be rebated to the Treasury, reducing the interest burden from the debt to the Treasury. Insofar as it is worried about inflation, the Fed could raise bank reserve requirements (on a fixed schedule) among other actions.
This option should have been discussed in the article. Japan's central bank has gone the route of holding large amounts of long-term debt for long periods of time. In spite of this fact, the country remains far more concerned about deflation than inflation.