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.
Not necessarily. If an atheist (example Boris Pasternak in Russia) speaks out against Stalin then he's an ally for those agitating for freedom.
However, you are correct that the Founding Fathers DID generally believe that religious beliefs will result in a better society than atheism. Even Jefferson espoused this. But Paine was condemned on his later actions, not his beliefs. Why wouldn't he have been condemned? He acted stupidly.