As much as it may disappoint you, this is *exactly* how the process is supposed to work.
Marriage is a state issue (which is why I laugh every time someone brings up the concept gay marriage, either for or against, at the federal level). Until the federal government starts issuing marriage licenses, it is up to each individual state as to whether or not to honor a marriage.
Why is this important, and why should the state care?
Marriage is more than just a piece of paper signifying that two people are joined together. Marriage grants certain rights as well:
1. Married couples (in most cases) cannot be compelled to testify against one another in a court of law.
2. Married couples gain special status under most tax codes.
3. Married couples are legally allowed to have sex (in states where adultery is defined as *any* sex outside of marriage, or places that still have breach of promise laws).
4. Married couples have preference in estate law over unmarried couples, in the event that there is no will.
5. Married couples are legally allowed to make life decisions for their partner in the event one is hospitalized - and they generally have higher authority than any other family member.
6. Insurance benefits, which are usually regulated by a state's laws, treat a spouse with higher preference than any other relationship.
With these and many other privileges associated with marriage, it is easy to see why a state has a say in who they grant these privileges to.
This is not a religious issue. If two people want to go to a church and get married - more power to them. They are free to do so. But if they want to receive all the benefits given to them by the state government for this marriage, they need to meet the state's criteria. This is why you have to go to a judge and get a marriage license if you want to receive the benefits granted by the state to a married couple.
So why do I say this is exactly how the system is supposed to work?
Since the state (as a representative of its people) grants special privileges to married couples, the people (through the state government) get a say as to who should have those privileges. These laws are not the same across the country, and reflect the heterogeneous nature of the US. Same sex marriage being legal in some states and illegal in others is one example of this. Another is the minimum age at which two people can legally marry. Another example are consanguinity laws that define exactly how closely two people can be related, if at all, and still be allowed to marry.
All these variables are dictated by the people who elect their representatives to state government.
As civics will teach you, a law passed by the state legislature (or put on the ballot by the people through the initiative process) can be trumped by the state supreme court. The state supreme court can be trumped by a federal court, or by the state constitution.
Since marriage is a state issue (and will remain so unless the federal government starts issuing marriage licenses), the federal supreme court has no jurisdiction in this matter. Therefore, opponents of gay marriage in California went through the state constitution.
I don't know California state law, but if it's anything like federal law, a constitutional amendment requires a large majority of either the legislature or the general populace to pass.
The point of the United States is majority rule, with respect to minority rights. Our governmental system was designed to honor that. In this day and age, we get so wrapped up around minority rights that we forget the concept of majority rule... the cornerstone of any democracy. Clearly, the majority has spoken in California.
As far as minority rights, note that there is nothing forbidding gays to get married in the religious sense - they are free to go to anyone who will perform a wedding ceremony. Nothing says they cannot live together.
However, until the people of California, as a whole, are willing to give them equal rights and privileges granted by the *state*, this is as much as they will get. It may be disappointing to some, but this is how our system works and it has served us well thus far.