May I Prepare Taxes for a Same-Sex Couple?

Yes. In such a scenario you are simply stating what is true according to civil law. They are civilly married and they are filing jointly. This would be the same with any couple that is in an invalid civil marriage.

Your preparation of their taxes does not, in my opinion, represent an approval or support for their civil marital status. When you prepare taxes for other civilly married couples that might be married for the wrong reasons, your tax preparation does not constitute approval and therefore neither would it in this situation.