It's really easy. Do those other than religiously ordained officiants (those authorized to sign a marriage license for states) get to decide now who they will and won't sign a marriage certificate for? If so, then there is no difference here. They choose to get authorized by the state to sign marriage certificates in a way that is non-religious (since, if it were religious, they would be ordained, not secular officiants of some sort). They cannot claim a religious exemption to performing a civil act in a secular capacity. Just as a civil servant working in a public office cannot refuse to give or file paperwork pertaining to same sex couples or interracial couples or interfaith couples. It doesn't matter if it is a marriage license or adoption records.
So far, all you've shown is that you have a particular political opinion on how you believe the Constitution should be interpreted. That is not in legal reality how it is interpreted.