That's the question that the Supreme Court said to the Prop-8 backers this morning, if I can be a bit tacky. Since Joe Citizen isn't directly harmed (other than being morally offended) by same-sex marriage, Joe doesn't have standing to appeal if the state isn't interested.
This does give governors a pocket-veto of sorts if they have a friendly judge to declare a ballot proposal unconstitutional; such a pocket veto can work on both sides of the aisle. For instance, if a animal-rights proposal gets taken down by a judge, no citizen has standing to sue for the pigs that are in too cramped quarters.
Not everything that's legal is right and not everything that's right is legal.
The DOMA case has more direct impact, since that should allow same-sex couples to make their marriages portable into non-SSM states and also allow them to use federal benefits to married couples. What we haven't seen yet is a case that would force non-SSM states to allow for them; expect that to be on the Supreme Court's desk next term.
Life goes on and government does some questionable things. Last I checked, they're not perfect.