This isn't meant as a utilitarian argument; the best possible defense of freedom of conscience in matters of religion is that it's not only repugnant to attempt to police the contents of people's minds, it is ultimately impossible. It is a nice side-effect that, if you leave people's beliefs be, there's often a free prize inside.
The counter argument is utilitarian (for varying definitions of "utility"): a person's conscious and actions have to be controlled, guided, or nudged. Otherwise results that are aesthetically unpleasing, unfair, or sub-optimal will come up.
Though for a religion to really mess things up they need to be hitched with a State. Hmm... maybe that's why it's part of the First. Though I suppose that's an axiom right there. "For X to really mess things up, they need the power of the State."
I'm reminded of this Glen Reynolds quip: "Those dangerous libertarians — they want to take over the government, and then leave you alone!"
For many, the idea of government leaving people alone is dangerous. Me, I'd prefer the robber barons, at least they just want money.
And a quote fresh today from Prof. Reynolds:
I don’t like this fatalistic attitude: “This is something that we’re going to have to live with for a while.” I miss the days when scientists told us we didn’t have to live with things like bloodsucking parasites.