First, I got my hands on the actual briefs from the San Francisco cases. As we guessed, California's expansive citizen-suit standing rules let the conservative groups sue to prevent the unlawful expenditure of government funds. (But query, as some professors are given to saying -- if the couples were reimbursing the city for all of its expenses, would standing still exist?)
Second, Steven pointed out a couple of techniques Congress could use to get around standing hurdles to the enforcement of the FMA -- most notably by suing the states itself or by offering bribes (techically "qui tam" actions) for people successfully bringing such suits, to be collected out of the treasuries of the states sued.
But that, of course, begs the next question: does the FMA contain an implicit repeal of state sovereign immunity?