Geof Stone makes a forceful argument, but it seems to me that there are two quite different strands to it -- strands that need to be separated.
At times, Geof is asking whether a "law [is] based on faith," whether a "law [is] based solely on sectarian religious belief," whether it "serves no legitimate public purpose." This category, he suggests, does not include laws that are "perfectly sensible law without regard to anyone's religious faith" or that have "a religious as well as a secular purpose," which would include a "moral-based reason" as well a "faith-based reason." Note that so far we're talking about the law.
At other times, though, he asks whether a person (including a political leader) backs a law "based entirely on his own sectarian religious beliefs," whether a person is "imposing [his] faith on others." That is a very different inquiry, an inquiry into the subjective motivations of a law's backers rather than whether the law in fact serves some public or moral purpose. For instance, I take it that all of us would agree that abolition of slavery, prohibition of alcohol, opposition to war, or support for civil rights are laws that have "moral-based reason[s]" as well as potentially "faith-based reason[s]." But all these laws were backed by some people -- perhaps many people -- for reasons that flowed from their own sectarian religious beliefs. (I chose these movements precisely because so many of their backers were deeply religious.)
In fact, I suspect that for many deeply religious people, all their moral beliefs are faith-based, because they believe morality only comes from God. I'd wager that many religious pacifists, abolitionists, and others would take precisely this view. Yet I think that we surely shouldn't condemn either their cause or them for this.
Your moral views may come from your understanding of human dignity; another's view may come from utilitarianism; another's may come from libertarianism; another's may come from fundamentalist Christianity. None of these bases are somehow provable; none is constitutionally superior to the others. (In fact, many of the arguments for religious freedom itself came from the "sectarian religious beliefs" of deeply religious people; I suspect that they supported religious freedom for religious reasons since religious reasons were the only moral reasons that counted to them.)
Any other approach is itself deeply discriminatory -- it suggests that atheists, agnostics, utilitarians, and the like are entitled to enact their moral views into law (because they don't rest on religion) while devout Catholics, Protestants, Jews, Muslims, and others are forbidden from enacting their moral views into law (because they do rest on religion). That's not mandated by the Constitution, it's not in my view compatible with our national traditions, and it's not right.
Hence my claim: It is certainly quite proper to ask whether a law is morally or constitutionally sound. A law banning the eating of pork may be quite unsound. Likewise, laws banning -- or allowing -- abortion, infanticide, the destruction of embryos or chimpanzees for medical purposes, or the killing of members of endangered species might be sound or unsound.
But it shouldn't matter whether someone supports them because of his belief that laws should turn on the greatest good for the greatest number, his belief that we are all sons and daughters of Gaea and must thus protect our environment, or his belief in the Bible. For most, quite possibly all, of us, our moral beliefs ultimately rest on unproven and unprovable moral axioms. The Constitution doesn't consign those whose moral beliefs rest on unproven and unprovable religious axioms to a lesser citizenship, under which they may not enact their views into law, while others with the same views that rest on unproven and unprovable secular axioms are free to do so.