Gays and lesbians seeking liberty and equality in their sexual lives, and religious conservatives seeking liberty in their religious lives, make fundamentally parallel claims on society. They each assert that some aspects of human identity are so fundamental that they deserve legal protection from all but the most important regulation. From a civil liberties perspective, they should be natural allies instead of bitter opponents. The one example where this shared interest has borne practical fruit is the Equal Access Act, which has protects the right of student organizations to meet in public secondary schools. The principal beneficiaries --the two groups that high schools most often seek to exclude -- have been Christian prayer clubs and gay rights clubs.
In other contexts, each side has tended to make the Puritan mistake, seeking liberty for themselves and regulation for their opponents. The conservative religious community has been the most obvious about this, criminalizing same-sex relationships when they had the political strength to do so, and now resisting same-sex marriage where they still have the political strength to do that. The gay rights side has responded not only by opposing conservative religious movements politically, but often by opposing their claims to religious liberty as well. Marc Stern has gathered many examples of gays litigating against religious liberty claims in his chapter of the book I helped edit, Same-Sex Marriage and Religious Liberty: Emerging Conflicts (Douglas Laycock, Anthony M. Picarello, & Robin Fretwell Wilson, eds., 2008).
Of course it does not violate anyone's religious liberty for a state to enact same-sex marriage, let alone civil unions. Nor does it violate anyone's liberty for religious conservatives to make what ever arguments they choose to offer against such legislation. We have separation of church and state, not separation of government from voters; religious citizens have the same right to speak and vote that the rest of us have. If bans on same-sex marriage are unconstitutional, it is because of the Equal Protection Clause or the Due Process Clause or the Ninth Amendment -- not because of anything in the Religion Clauses.
What does violate religious liberty is unnecessarily forcing conscientious objectors to celebrate or facilitate same-sex marriages. This is not just a matter of providing that churches, synagogues, and mosques need not perform weddings that they disapprove of. They surely have that right under the Free Exercise Clause, even under the Rehnquist Court's stingy interpretation of the Clause. What needs to be provided by legislation is the right of religious organizations and individuals not to support or assist same-sex marriages in other ways that violate their religious commitments.
Must a church counseling agency, or an individual religious counselor, counsel same-sex couples and help them preserve a relationship that the counselor considers sinful? Must a wedding planner with religious objections help them plan the event that creates and celebrates the relationship? Must a religious adoption agency place children with same-sex couples?
The answer to all such questions should be no, so long as there are others willilng and able to provide the needed service to the same-sex couple. Clear exemptions to this effect protect religious liberty; they are also in the interest of same-sex couples. To impose legal penalties or civil liabilities on such consientious objectors will simply ensure that conservative religious opinion opposed to same-sex marriage can be repeatedly aroused to fever pitch. Every such case will create a martyr to rally around and new talking points for demagogic opposition to same-sex marriage.
It is much better to enact same-sex marriage with broad protections for religious liberty and let the emerging ordinariness of same-sex marriages, and the economic incentives of the free market, do their work. The number of people in the business of assisting marriages who assert their right to conscientious objection will be small and declining. Many Americans are morally opposed to same-sex marriage, but a much smaller number feels personal responsibility for providing services to others who are engaged in the conduct they consider immoral. As same-sex marriages become familiar, and as they turn out to be harmless to opposite-sex marriages, and as the older generation retires, the number of people willing to turn down business as a matter of conscience will get steadily smaller. It is not in either side's interest to coerce religious objectors into facilitating same-sex marriages in ways that violate their conscience.
The religious liberty provision in the Illinois civil unions bill is badly drafted, consequently ambiguous, and open to narrow interpretations even with respect to religious organizations. It clearly does nothing to protect religious individuals. It needs to be rewritten, but that is beyond the scope of this post.
I support same-sex marriage, and I support religious liberty. They need not be inconsistent, if we will just pay attention to the religious liberty issues.