It's too bad people like Thomas Young and the founders believed in violent revolution. It set a bad example for communists to follow in the 20th century.
I don't believe that Thomas Paine's Rights of Man is excluded from government canon because he was a Deist. It is excluded because it promoted a radical notion of rights—that is, as being excluded from aliens to the social contract (ie Indians, Slaves) by the contract itself. The reason government today still abhors it is because it is a negative definition of rights, and therefore implies that enumeration of rights under the letter of the law will only further degrade liberty for non-participants.