Your friend is seriously mis-interpreting the Treaty of Tripoly, which in essence declairs “Peace and Friendship” between the US and the Bey of Tripoli and his people. The particular clause usually cited in the treaty by anti-religionists merely states that the US is neutral vis a vie Christianity and Islam.
The Founding Fathers were mostly practicing Christians. However, at the time of the Second Colonial Congress, which produced the Declaration of Independance, The Church of England was the official State Religion of most of the colonies, with the exception of Pennsylvania, which was Quaker, Maryland, which was Catholic, and Connecticut and Massachusetts, which were Puritan.
Fast forward the the drafting of the US Constitution. The Founding Fathers realized that to be fair to everyone, the Government had to be neutral with regards to religion. Therefore, the First Amendment of the US Constitution guarantees Freedom of Religion, right alongside Freedom of Speech. The vast majority of the founders who wrote and voted in the Bill of Rights were practicing Christians, or as it was called back then, Deists.