Yes, but separationists need to be careful in explaining the historical background of this treaty.
In 1797, six years after the adoption of the Bill of Rights, the United States government signed a treaty with the Muslim nation of Tripoli that contained the following statement (numbered Article 11 in the treaty):
So far as we can tell, the inclusion of these words in the treaty had no negative political ramifications for the treaty whatsoever. On the contrary, the treaty was approved by President John Adams and his Secretary of State Timothy Pickering, and was then ratified by the Senate without objection. According to an information sheet provided to us by Ed Buckner of the Atlanta Freethought Society:
Accomodationists frequently note that Article 11 appeared only in the English version of the treaty; in the Arabic version a letter-like page of gibberish appears where Article 11 should be. The Arabic version was translated by Joel Barlow, the diplomatic representative that negotiated the treaty on behalf of the United States. Barlow was a good friend of Thomas Jefferson, Thomas Paine, and James Monroe, and was most likely a deist or atheist. It is almost certain that he authored Article 11 in the English version. Many accomodationists seem to think that the absence of Article 11 in the Arabic version has something to do with Barlow, and that this absence should somehow blunt the separationist impact of the English Article 11.
In point of fact, we have no idea if Barlow is connected to the page of gibberish in the Arabic version. The "substitute" page was not discovered until 1930; what happened to the treaty before that time is unknown. The Article, if it was originally in the Arabic version, could have been lost at any time between 1797 and 1930. And there is certainly no reason to assume that Article 11 wasn't in the original Arabic version: A Muslim nation would surely have welcomed Article 11 as an assurance of American intentions with respect to religion.
More generally, we can't imagine how the absence of Article 11 in the Arabic version effects the separationist argument. It was the English version of the treaty that was approved by President Adams and Secretary Pickering, and this version unquestionably contained Article 11. Similarly, when the Senate ratified the treaty, they did so knowing full well that the English version declared that the United States was not a Christian nation. The separationist implications of the treaty can't be escaped by arguing that the Arabic version may not have contained Article 11; the President, Secretary of State, and Senate thought it did, but approved the treaty anyway.
The treaty of Tripoli remained on the books for eight years, at which time the treaty was renegotiated, and Article 11 was dropped.