The issue of marriage has been under state - not federal - jurisdiction ever since this country was founded. The states have decided who they wanted to allow to get married for hundreds of years, and the federal government has respected this jurisdiction by recognizing all marriages performed by these states. But in 1996, this all changed, and the Federal Government inserted themselves into the marriage issue by passing the Defense of Marriage Act (DOMA). This law specified that only marriages between a man and a woman would be recognized by the Federal Government, no matter what the states did regarding the marriage equality issue. As many know, this law is winding its way through federal courts and has been deemed unconstitutional by said courts because it violates the states historical right to determine who is and who is not married. The decisions are not about "gay marriage" per say, but it is about the level of federal control that should be allowed in a states decision.
The Obama Administration recognizes this fact; and it is one reason why it is fighting so hard against DOMA. In principle, in order to be consistent with their position on DOMA, they would also have to fight against a federal law that mandated national marriage equality; because that law violates the very essence of state jurisdiction over marriage.
Not all see this view of State jurisdiction as legitimate, and some - such as former Clinton advisor Richard Socradies - go so far as to say that it is fundamentally anti-American. He stated, as quoted by ABC news,
This states' rights argument is a separate but equal argument. Would the president have thought it right to let the states decide on the issue of interracial marriage, or on whether or not women should be allowed to vote?This argument, though it may seem correct, is actually a red herring. You see, it asserts that if the Federal Legislative and Executive branches went with a "states rights" approach, we would see separate by equal treatment - using, for example, anti-miscegenation laws. Though it is true that anti-miscegenation laws created a patchwork of marriage rights in the states, in making this argument, Socradies fails to recognize the difference between a Legislative/Executive branch passing a law, and rights gained under the Constitution. If state law violates the federal constitution, then it must be struck down, because the Constitution is the supreme law of the land, above both state and federal governments. This is why, for example, anti-miscegenation laws were struck down, because of their violation of the 14th Amendments equal protection clause. But, when the Legislative and Executive branches invade the arena of states rights in regards to marriage law - whether pro- or anti-marriage equality - with federal legislative law; that ALSO violates the Constitution, per the 10th Amendment. Thus, if anti-gay state constitutional amendments violate the Constitution, then yes, they can be and will be struck down (just like anti-miscegenation laws), and the Court has that authority. But at the same time, until then, the federal government must respect the limits of its Constitutional authority, and not infringe upon state jurisdiction to do what it wishes, a position that the Obama Administration is holding to quite well.