Apparently there are rumors flying around (after a recent Novak column) that Clement was forced out, because his brief in
Heller was in opposition to the President's feelings on the issue. If true, it would explain the timing of the resignation.
The issue is discussed a bit here (with the typical Slate perspective on this):
http://www.slate.com/id/2185927/pagenum/all/
Not that this would be a huge problem for Clement; he's going to get a boatload of money from some firm (maybe King & Spalding or Kirkland), and he's still a possible future Supreme Court pick.