Providing marriage certificates is in no way condoning gay marriage. All she is doing is providing paperwork that is granted by the government.
If it were a private business, this would be a different matter. However she works for the government and should act according to federal laws.
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According to Christians, marriage is an institution of God. Homosexuality is offensive to his institution according to the Bible. Providing marriage licenses as a Christian to gays would be in direct violation of their religion