So It boils down to the church having the final say on what constitutes a marriage. "Marriage would be between couples and their church"
You complain when the state gets to define what constitutes a religious belief when it comes to health care. Yet, under your formula you advocating that the church can exclusively define marriage.
So atheists miss out. Alternatively if they really wanted a marriage and not a civil contract they could get married in a church and look like hypocrites. But this would be the price ones needs to pay.
This is like the price one needs to pay when one has their religious beliefs defined by the Healthcare Act.
Tut