The Founder' don't appear to have usesd their religious beliefs as the litmus test of who was with them or against them during the revolution. Why do you think we ought to do it now?
The US was friends with Stalin during WWII also in order to defeat the overwhelming evil of the time. But we dropped him like a hot potato when more of his intentions became known later.
You seem to assume the Founders had some kind of all-seeing power to know what Paine would do and say in coming decades.
I don't think his religion is the litmus. It's what he did as a result of his beliefs that tell the story.