Did Supreme Court justice Joseph Story ever say that, at the time of the adoption of the Constitution, there was near universal consensus that "christianity ought to receive encouragement from the state?"

Joseph Story was an Associate Justice of the Supreme Court from 1811-1845, and the most important legal commentator of his day. In 1851, while serving as the Dane Professor of Law at Harvard University, he published his Commentaries on the Constitution of the United States, which included a short section on religious liberty. In the opening pages of this section Story argued for the importance of religious faith for good government, and then proceeded to claim that:

Probably at the time of the adoption of the constitution, and of the amendment to it, now under consideration [i.e., the First Amendment], the general, if not the universal sentiment in America was, that christianity ought to receive encouragement from the state, so far as was not incompatible with the private rights of conscience, and the freedom of religious worship. [p. 593]

Accomodationists sometimes use this statement as proof that the Constitution could not have been intended to prohibit federal support for religion. But this is to misread Story's claim. All Story is claiming here is that, at the time of the adoption of the Constitution, there was widespread sentiment for aiding Christianity. What Story does not claim here is that the Constitution empowered the federal government to give such aid. Indeed, only a few pages latter in his Commentaries he explicitly denies that the federal government had such power:

It was under a solemn consciousness of the dangers from ecclesiastical ambition, the bigotry of spiritual pride, and the intolerance of sects, thus exemplified in our domestic, as well as in foreign annals, that it was deemed advisable to exclude from the national government all power to act upon the subject. The situation, too, of the different states equally proclaimed the policy, as well as the necessity of such an exclusion. In some of the states episcopalians constituted the predominant sect; in other presbyterians; in others, congregationalists; in other, quakers; in others again, there was close numerical rivalry among contending sects. It was impossible, that there should not arise perpetual strife and perpetual jealousy on the subject of ecclesiastical ascendancy, if the national government were left free to create a religious establishment. The only security was in extirpating the power. But this alone would have been an imperfect security, if it has not been followed up by a declaration of the right of the free exercise of religion, and a prohibition (as we have seen) of all religious tests. Thus, the whole power over the subject of religion is left exclusively to the state governments, to be acted upon according to their own sense of justice, and the state constitutions; and the Catholic and Protestant, the Calvinist and the Arminian, the Jew and the Infidel, may sit down at the common table of the national councils, without any inquisition into their faith, or mode of worship. [pp. 596-597, emphasis ours]

Story, in other words, believed, along with Madison, Jefferson, and a host of other framers, that the Constitution gave no power to the federal government over religion. With respect to the federal government, Story was a separationist. Accomodationists quote him out of context when they reproduce his general statements, but not his specific claim that the federal government has no authority over religion.