Bad analogy in this case. That analogy would work in the case of the Christian baker if, for example, the baker refused to sell cookies or brownies to homosexuals rather than just refusing to bake a wedding cake. The city might have a case if the pastors regularly rented out the chapel for weddings where other people would perform the ceremonies, but refused to rent out the chapel because these people were homosexual. (Notice I said "might" have a case - I would argue against that as well, but the courts might feel differently.)
In this case, you have a city trying to force a licensed minister to perform a religious ceremony that would violate his conscience and religious beliefs. It is requiring the minister's personal participation in what he considers to be a sinful act that makes this so egregious. (I feel the same way about the bakers and photographers who have been sued.) And that is exactly the goal of these deviants and their supporters - to try to force Christians to be participants in their sin, or put them out of business otherwise.
Here is an example that illustrates my opinion. The minister at my church will not perform a same-sex marriage as part of the “religious services” offered by the church and I don't think the government could force him to perform one in that context. However, if the church ran a for-profit business on the side advertising weddings to the general public and my state had legalized same-sex marriages, I don't think the for-profit side of the church could legally turn them down.