good question!
factors like involvement, responsibilities and perhaps even whether one is far more content than the other seem like important considerations.
also, i have a general theory for decision making and resolving conflict that i like to use in any scenario, and this one certainly could apply.
which person cares the most? meaning, who feels this outcome more? i have been using this argument for a long time now, when grandparents moved in with me.
even though it was my first house, and i really wanted to have my kitchen exactly as i wanted it, i quickly realized that the organization and details of what we did differently would have FAR more impact on my grandma than on me. at that time, it was a lot easier to simply compromise knowing that i was sparing her much more discomfort, pain, difficulty that i would be feeling were the opposite outcome decided.
i would venture to say that one person of the two is going to have far greater depth of feelings on the matter. those concerns should be weighed heavily and then a decision can be made together.
also, i agree that they definitely should have ONE home church. but i do think it would be sensitive and considerate to make an effort to visit and occasionally attend events at the old church (the church that was abandoned in favor of the alternate) so that those relationships can be maintained (or even expanded upon, as a couple).