'pro-atheistically' originates from a combination of the prefix 'pro-' (Latin via Old French), meaning 'for' or 'in favor of', and 'atheistic', which comes from Greek 'atheos' meaning 'without god' plus the adjectival/derivative suffix '-ic'; the adverbial ending '-ally' (from Latin/Old French '-alis') forms the adverb.

'pro-atheistically' developed from the adjective 'pro-atheistic' (formed by 'pro-' + 'atheistic') with the addition of the adverbial suffix '-ally'; 'atheistic' itself derives from Greek 'atheos' -> Latin/Medieval forms -> English 'atheist'/'atheistic'.

Initially the elements meant 'for' (pro-) and 'without god' (atheos); combined they have come to mean 'in favor of atheism' and the modern adverb expresses doing something in that supportive manner.