Unless you live in a state with full-fledged same-sex marriage, your HR dept. is still going to have to differentiate.
Last I checked, the composition of the Senate had a pretty big impact on who gets into the judicial branch of the US government.
Although gay marriage was previously legal in California, between all the legal challenges and the passage of Proposition 8, it didn't become fully normalized for legal purposes (ie regulations that are indirectly affected by marriage laws). Now that process will resume.
In any case, implementation of the CA Supreme Court's decision could not go ahead until the USSC had issued its decision; now the state is free to promulgate new rules.
The case concerning California’s ban on same-sex marriage, Proposition 8, was decided on technical grounds, with the majority saying that it was not properly before the court. Because officials in California had declined to appeal a trial court’s decision against them and because the proponents of Proposition 8 were not entitled to step into the state’s shoes to appeal the decision, the court said, it was powerless to issue a decision. That left in place a trial court victory for two same-sex couples who had sought to marry.
I'm belaboring the point to make clear that the Supreme Court did not rule on Proposition 8 itself.
The actual decision that can now be implemented is a decision of the US District Court for the Northern District of California (a federal trial court that struck down Prop 8 as a violation of the federal Constitution), not the California Supreme Court (the state appellate court who upheld the Proposition as a valid Constitutional amendment and not an improperly-passed Constitutional revision under the State Constitution.)
Section 2 of DOMA expressly released states from the requirement to recognize other states' gay marriages, but if it's struck down, "Full Faith and Credit shall be given in each State to the public Acts, Records, and judicial Proceedings of every other State."
So why wouldn't marriage apply? If it doesn't, I suspect this will be the target of new legal challenges.
[ETA: Apparently Section 2 of DOMA was not struck down. Sorry about that.]
But, IIRC, recognition of out-of-state marriages without conditions has never been required by the Full Faith and Credit Clause -- this was actually one of the arguments against Section 2 of DOMA.
Though federal benefits cannot be denied to married same-sex couples, state benefits can be if same-sex marriage isn't recognised in the state.
This still presents some headaches for some people and even the most well-meaning of employers.
For instance, imagine if you have a same-sex couple living in a state that doesn't recognise SSM (say, Wyoming) but who married in a state that does (Washington State). One of the two is working for a company just across the border in Washington State, but the other doesn't. Now imagine that the state provides health coverage while a person is unemployed, but it doesn't cover people whose partner's employer provides healthcare. Is the employed partner's health insurance liable for treating his unemployed partner or is the state liable to provide coverage?
What about when a couple is travelling? Is a gay partner covered by their partner's health insurance when visiting a state that doesn't recognise SSM? What about states that have civil unions rather than full SSM?
In Britain, it has been discussed a fair bit this week that even though since 2004 we've had civil partnerships which are supposedly "marriage in all but name", gay people in civil partnerships are still not getting fair treatment regarding pensions. As an openly gay man who might as some point want to get married, I've followed the news and discussions around the legislation on same-sex marriage in Britain fairly closely and I still don't know what the situation with pensions is, but apparently it's still broken.
I think things will be in a bureaucratic mess for a while. It'd probably be easier if it could be legalised across the whole country in one fell swoop... but that might just be wishful thinking on my part.