All rulings have effective dates. I'm not sure why 9/16 is the one for this ruling, but it is. If the couple was married in 2012, then there are several possible scenarios:
The couple already filed as single/single for federal (in CA they've filed a joint return for the state since 2007 whether married or RDP). These couples have the choice to amend if beneficial, but don't have to. They filed under the laws as effective at the time of filing. This is the difference for same sex couples and het married couples.
The couple is on extension. They can file MFJ/MFS or have a window up to 9/16 in which the old laws can pertain. Planning, estimates, extension payments were all based on the law of the land as effective at the time the extension was filed. This may be the reasoning for the window.
The couple was not married in 2012, but has since gotten married. They will have to file MFJ/MFS for federal for 2013. They were single in previous years and do not have the ability to amend back years.
The Supremes did not rule that same-sex marriages are only recognized since the date of the ruling. DOMA, which prohibited the feds from recognizing marriages performed legally in the states or other countries was tossed out as unconstitutional and discriminatory. Same-sex couples have been legally married in many other countries and several states for many years. Like any other situation where one may have filed where the law is being litigated (remember sales of stock received in demutualization? That was litigated for years and the IRS position was not what the courts finally decided), once the courts have ruled, amendments are permitted.
Allowing amendments also follows every other pronouncement regarding SSMCs. When the feds were required to recognized CA community property law in the case of SSMCs, amendments for open years were allowed but not required.
Two states who do not have same-sex marriage but whose return calculations begin with federal and require the same filing status as federal have already said that SSMCs should use the same filing status as federal (Virginia & Utah).