Separation of church and state is one of those concepts that is discussed frequently and understood infrequently. Despite ample evidence to the contrary, it has mutated to mean that any and all religious sentiment in the sphere of governance is entirely inappropriate. Not only does this directly conflict with the free speech elements of the First Amendment, it also tramples upon the free exercise of religion.
The debate largely swirls around a response from Thomas Jefferson to a group of ministers from the Danbury Baptists Association. What is frequently left out, however, is the orignal letter that prompted it as well as historical context. Jefferson's response was to assure the ministers that there would be no official national church or religion and that, at the federal level, the rights of religious worship were seen as inalienable and immutable, unlike the state of Connecticut at the time. He was also careful to not speak as to the state's ability to choose a state religion even though he authored the Virginia Statue for Religious Freedom that forbade such actions in his home state. The matter as a whole can hardly be reduced down to a phrase from a single letter and is no simple matter of black-and-white.
If we do, however, presume that Jefferson intended the contemporary meaning of the phrase (unlikely, but this is a hypothetical situation), then we must ask ourselves at which point do we stop invalidating another's opinion on the sole basis of theological backing. After all, movements such as the Revolutionary War, abolition, women's suffrage and civil rights began in and/or were cultivated by churches. Many state bans on gambling have roots in religious beliefs despite being backed by empirical data. State-run liquor stores (which are found in Vermont, Pennsylvania and Alabama, among other places) were often the result of the prohibition movement's toughening of liquor laws; many of them relied on scripture rather than case studies as their motivation.
There are also laws on the books against polygamy and incest, even if consensual, whose roots are found in biblical law. Because of this, should we discard such prohibitions? Obviously not. The vast majority of citizens are strongly in favor of such prohibitions and the laws of each state must be largely in congruence with popular opinion lest we slide into tyranny. So long as the fundamental rights guaranteed by the federal and state constitutions are not being infringed, the courts have overwhelmingly ruled that states (and the federal government, in the case of territories) have wide latitude in passing laws to protect and strengthen public morality when there is a compelling state interest. This was the reasoning of the court when they found that federal laws prohibiting polygamy in territorial Utah were not an infringement upon religious exercise by the Mormons living in the area.
It is also unreasonable to expect every person of religious faith to put that faith to the side when deciding upon the laws of the land. Such a declaration, in effect, says that you must be an atheist or secular humanist when politics is involved. It is an attempt at forcing state religion through the backdoor, the state religion of no religion, and unfairly subjects people of faith to de facto religious tests. Such principles are often applied unequally depending on the issue. Rarely is the cry of "separation of church and state" heard when faith backs an action of the political left, but we hear it very frequently towards the actions of the political right. Ministers on both sides of the spectrum are starting to rebel against these muzzles upon their ability to speak out on the issues of the day as their forebearers would have.
Instead of attempting to silence political opponents with a simple-minded catchphrase, we should be trying to encourage a discussion and dialog between the various sides of an issue. In that process, you cannot ask your opponent to discard a vital aspect of their very being while not being held to the same standard. It is disingenuous and only promotes attempts to shout over the other side. I, for one, will refuse to abide by any attempts to invalidate my opinion simply because I have a theological basis for it.