Opposition to the Catholic Church in Revolutionary France was not, I believe, motivated by atheism as it was by anticlericalism. Rather than focusing on personal beliefs, anticlericalism focused much more on the abuses of the Catholic clergy, the Church's support for the Ancien Régime and its role as a social repressor.

Whilst in Revolutionary France this did mean that there was some overlap with positivist / rationalist / atheist beliefs developed during the so-called Enlightenment, anti-clericalism has much older roots in 15th and 16th humanist and Reformation thought. Christopher Hill's book The World Turned Upside Down highlights a number of groups during the English Civil War who were both anticlerical and radical. Anticlericalism also re-emerged as a form of sociopolitical opposition to the Church across Europe in the nineteenth century.

So whilst personal beliefs in God / science may have been important for some, I would see anticlericalism / atheism in Revolutionary France as an articulation of a political position which focused on the Revolutionary potential of the lower classes to overcome the oppression of the monarchy and church.

Similarly, the counterrevolutionary War of the Vendée (1793-6) was not simply about repressing atheist beliefs but also an attempt to quash the Revolution and restore the Ancien Régime.