Same-Sex Marriage and Religious Liberty: A question for Michael

I share Michael P's admiration for Prof. Doug Laycock, and so I take very seriously Doug's remark, to which Michael linked:

The nature of marriage is a question with profound religious significance and fundamentally disputed answers.  The state has no more business imposing a single answer to that question than to any other religious question.  Marriage is for the churches; government should confine itself to civil unions.  And then we should try as best we can to create rules that enable Americans with fundamentally different views of marriage to live in peace and equality in the same society.

I'm going to bracket, for now, the possibility that, for public-policy purposes, the state might well have entirely non-"religious" reasons for believing (and legislating on the basis of the belief) that the public good would not be well served by a move to a civil-union regime (assuming, as I gather Michael does, that such a regime would not distinguish between same-sex and opposite-sex couples). 

What are the "rules" -- to which, I gather, Michael is offering his "Amen" and support -- that would "enable Americans with fundamentally different views of marriage to live in peace and equality in the same society"?  They would need to reflect, it seems to me, a thorough-going commitment by the public authority to *genuine* respect for those persons and institutions who do not believe that same-sex unions and marriage are morally equivalent.  What would be the approach, in such a regime, then, to (just to pick two examples) (a) tax-exempt status for organizations that "discriminate" against same-sex unions, and (b) the applicability of non-discrimination laws to such organizations' hiring-and-firing practices?