Substitute this question:
Why would a former general oppose a Joint Chiefs of Staff decision on a matter of military strategy and not respect the wisdom of the military and honor our system of separation of powers?
for this question:
Why would a law professor oppose a Supreme Court decision on a matter of constitutional law and not respect the authority of the Court and honor our system of separation of powers?
Although the blogger who poses the second question (Ann Althouse, whom I quite like) implies that the answer is so complex as to require a separate post, I must admit that Althouse's question seems as silly as the one about generals. Nevertheless, I'll stab at an answer here and now:
Because he thinks the Court is wrong.
While I personally believe that the Supreme Court got the central question right in Citizens United v. Federal Election Commission, I also believe that the President, and Congress, have an independent duty to interpret and attempt to apply the Constitution.
Regarding separation of powers, it's worth noting that virtually all of the founding fathers, with the possible exception of John Marshall, believed that the President and Congress had such a duty.
Part of what's wrong with this country is that Presidents and the Congress (as with George W. Bush who believed McCain-Feingold was an unconstitutional restriction on free speech, but signed it anyway because he believed the Court would veto it for him), abdicate that duty. Presidents take their duty to control the military seriously. Why shouldn't they accept their duty to execute the law, in accordance with the Constitution, with equal seriousness?
George W. Bush was a coward. In this respect, ex-law professor Barack Obama is a President who takes the duties of his office seriously.