In part I share my esteemed colleague's dismay at the rancor between secular and religious liberals, but I do not think his challenge, though powerful, will settle the matter. I certainly understand Allen Brill's weariness, though I think he overestimates the personal component: he is not the problem, it is structural. A part of the problem is definition, as it so often is: there are really three different debates going on, but without separating them out we will continue to carom back and forth between topics without resolving anything.
The first thing that should be noted is that secular liberalism owes a great deal to religion. If Catholics and Protestants (and Deists and Atheists) didn't need a neutral way to talk to each other and live with each other, I'm not sure that a secular state would exist at all. And the contradictions between competing but coexisting theologies created the space within which critical secularism could emerge. Whether this redounds to the credit of"religion" as concept is your own personal Rorschach test: I really don't care what moral weight you give it as it is simply historical fact.
Second, I think it is entirely possible, and very important, to disagree vehemently with civility. Some people don't think that's possible where religion is concerned; some people don't think it's possible where politics is concerned; I think they're all wrong, but that doesn't make them bad people.
Theology as Public Policy: Bad Idea
Public policy needs to be based on public good, and inflexible ideologies are bad tools for developing public good. This is true whether it is a secular ideology (Ralph Luker has cited the French Terror, Stalin and Mao, as usual) or a theology (and if it weren't for secular liberalism, there'd be a lot more theocracies to point to as bad examples) or an irrational hardened nationalism (which has replaced theocracy in most cases, anyway, subsuming religion as a component of identity). Theology is good for developing values, but the base texts and even the core ideas of most religions permit far too much interpretive freedom to translate into definitive policy directives. Not to mention the problem of picking which theology; if you don't pick a specific one, you're back to the problem of interpretation and selectivity again. Oh, and we're not all the same religion anymore, either. Actually, I don't think there's a single modern state that can claim absolute uniformity of religion.... except (maybe) Vatican City.
Religious Rhetoric in Public Discourse: Fine, Within Limits
I'm a big fan of metaphor and analogy and simile and storytelling and quoting (paraphrasing, stealing, adapting, reclaiming, whatever) from good material. These things enliven our language and deepen our meaning, sometimes with clarity and sometimes with nuance. The problem is when the language is not rhetorical, but literal: faith is not proof."Jesus said 'feed the children'" is a nice chorus line for Tom Paxton's song"Feed the Children" [track five], but it's not proof that the state should be involved in feeding children. It may be enough for the faithful to advocate feeding children, but it's not proof in and of itself outside of the community of the faithful. Another problem arises when the nuances and implications are positive for some and negative for others: an American politician quoting biblical references to Israel to an American Jewish group could offend American Palestinians, for example. Finally, because the state should be a neutral party with regard to religion, people and institutions of actual power need to be particularly cautious about using language or symbols which are exclusive or which could be seen as coercive (see previous example, or ex-judge Ray Moore). A willingness to apologize when offense has been unintentionally given, then brought to attention, and a willingness to accept apologies and clarifications, would help considerably. There's gray areas to enjoy here, but smaller, I think, than most people realize.
Religious Communities in Political and Social Movements: Powerful but Independent
As Ralph Luker correctly points out, religious movements have had a powerful role to play in just about every major successful American progressive movement. (Nobody has contradicted him yet; I tried but, not being an Americanist, failed.) He doesn't point out that they've also been active in major regressive movements (segregation comes to mind, and the anti-abortion movement, Creationism in science curricula), that there are significant religious movements that support both parties, and none that will claim absolute allegiance to a political movement (though that might be a function of our tax law). That's the essence of the problem, of course: religious movements are, by definition, not single-issue, not loyal to political parties. Religions are independent, with their own sense of right and wrong and goals that go well beyond political and social change. I think activists who seek social and political change are wrong to reject religious views and participation outright, but they have the right and good reason to treat those views and that participation tentatively and cautiously. Religious leaders do the same with secular activisms, accepting them and supporting them only when they are a good fit with their values and goals.