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.
The assertion seems to be that it's an inevitable consequence of his religious beliefs. If you do not hold the correct religious beliefs, you either are or will inevitably become hostile to the cause of preservation of the republic.