The accommodationist argument glosses over considerable evidence suggesting that Congress did not want to directly support religion in the Northwest Territory. Consider, first, that Article I of the Ordinance contains an explicit guarantee of religious liberty: "No person, demeaning himself in a peaceful and orderly manner, shall ever be molested on account of his mode of worship, or religious sentiments, in the said territory." Note, in particular, that this language is drafted to highlight the individual's right to religious freedom, and that it is far more explicit than the first sentence of Article III.
Second, Congress twice rejected attempts to insert direct support language into earlier versions of the Ordinance. In 1785, for example, a Congressional subcommittee considered a completely secular draft of the Ordinance authored by Thomas Jefferson. The subcommittee included a number of representatives from the New England states who strongly favored state support of religon. The committee proposed a plan that would have set aside lot number 29 of each township established in the territory for the support of either religion or charitable purposes (as determined by the majority in each township). Happily, Congress defeated both the proposal and the ordinance by one vote. James Madison's adverse reaction was particularly notable. "How a regulation so unjust in itself, so foreign to the authority of Congress, so hurtful to the sale of public land and smelling so strongly of antiquated bigotry, could have received the countenance of a committee is a truly a matter of astonishment" (Richard B. Morris, The Forging of the Union: 1771-1789, pp. 172-173, our emphasis).
The second attempt to insert language directly supporting religion occured in 1787. Congress was drafting a version of the Ordinance that included Article III without the controversial first sentence discussed above. During the drafting process, Congress was approached by The Ohio Company Associates, a group of New England revolutionary war veterans turned land speculators, who wanted to purchase a million and a half acres of land in the Northwest Territory. The Ohio Company was lead by the colorfull Manasseh Cutler, an ex-army chaplain, skillful lobbyist, and staunch supporter of the New England tradition of direct state support for religion.
At Cutler's insistence (and capitalizing on Congress' desire to dispose of the land), the Congressional New England voting block inserted into Article III language providing for the support of religion. They proposed the phrase, "Institutions for the promotion of religion and morality, schools and the means of education shall forever be encouraged." Congress, however, appeared to balk at the proposal and softened the language to remove any reference to the support of religious institutions. The result was the version of Article III that we have been discussing in this webpage (Richard B. Morris, The Forging of the Union: 1781-1789, page 173ff.).
If Congress had wanted to provide for religious aid to schools in the Northwest Territory, they could have easily done so in the Northwest Ordinance. In fact, the record indicates that they twice defeated proposals to authorize such aid. While Manasseh Cutler was successful in getting Congress to agree to language that linked education with religion, this language did not explicitly authorize government support of religious institutions and, hence, fell short of what he wanted. Accommodationists, in other words, simply cannot build a case for non-preferential aid on the basis of the text of the Northwest Ordinance.