OK, if the atheism debates are so squalid, then what's the moderate, "philosophically respectable" approach to some of the issues that come up in them?
A recent episode of the University of Chicago philosophy podcast Elucidations featured philosophy uber-blogger Brian Leiter (who taught my philosophy and the law class at U. Texas). Leiter addresses the question, "Do matters of religious conscience deserve special protection in law?"
His answer is a qualified "no," in that yes, matters of conscience deserve protection, but not in virtue of their being associated with a religion. Of course there are historical reasons why we needed special protections for religion, and certainly it's easier, when faced with someone who claims that he can't follow the law due to a matter of conscious, to procure evidence that the person isn't just lying if he is associated with an established religion (e.g. Quakers have predictable anti-war beliefs), but ideally, we should broaden the law to provide some protection for all matters of conscience and omit the reference specifically to religion.
This is part and parcel of new atheist claims that religion gets undue deference both socially and legally, and it's ironic that a group that often decries "special rights" for homosexuals (when the issue is, of course, merely guaranteeing them equal rights) is itself singled out for special protection as a matter of Constitutional law.
Leiter provides a more moderate tone, though, and suggests a working definition of religion that sounds like Sam Harris's but is phrased as value-neutral: a view is religious when at least some of its claims are purposely insulated from the typical standards of justification that the rest of our beliefs are supposed to be subject to. In other words, at least some claims need to be taken on faith. Second, the system must make categorical demands on action: typically moral action, but other kinds of action too (e.g. how to dress).
Leiter provides a number of insights about the interaction between religion and law; for instance, given his definition of religion as issuing categorical demands, it follows that religious folks will (if they are strictly religious) be particularly resistant to society-level madness like Nazism or the red scare, though the same stubbornness can of course point in a radically wrong direction as well.
Another good conceptualization is the distinction he makes between recognition respect and appraisal respect: though we have the duty to "respect" each others' religion in the sense of recognizing that we all have the right to our opinions, particularly on matters of conscience, this doesn't entail that we have to actually respect their opinions in terms of assessing them as to any degree correct or wise. Tolerance, for Leiter, is all that's required to do our civic duty here.
The Elucidations method is to interview U. of Chicago faculty and alumni about things they're working on. The interviewers (including Matt Teichman, who's tentatively agreed to come on P.E.L. to talk about Frege with us!) ask some leading questions but more or less let the interviewees go on and on as long as they want. In some cases, this can be messy, but Leiter does a great job keeping things clear and cogent. It was great to hear him speak again (and makes me feel a bit better about how mean he sometimes is on his blog).