I have no problem with writing in a fairly broadly worded religious exemption into gay marriage laws if that'll get churches to sign on with the thing, although I also do believe the concerns as stated in this article are overblown. Particularly this one:
SSM increases the number of occurrences in which traditionalist religions or believers might be asked or pressured to facilitate same-sex ceremonies as organizations or business owners. Beyond that, SSM eliminates the argument, which has sometimes been successful, that a traditionalist organization does not engage in sexual-orientation discrimination as such, but acts against all extramarital sexual conduct. See, e.g., Christian Legal Society v. Walker (7th Cir. 2006) (accepting this argument for CLS's limits on holding leadership positions). Therefore traditionalists in some places will be newly subject to the claim that they are committing sexual-orientation discrimination -- or committing marital-status discrimination, if they act based on an objection to an individual's having entering into a same-sex marriage.
The first point is foolish... you don't have a right to not be asked to do things you don't want to do. Say "no". It's true that if gay marriage is legalized more gay couples will ask their pastors to marry them at which point their pastors might be in the regrettable position of having to out their organizations institutionalized homophobia. Cry me a river.