What pisses me off the most about Space Marine atheism is they don't have anything to offer in replacement to religion other than 'muh reason', as if that in and of itself was truth. There's no discussion of non-theological philosophy, just 'muh reason'. Ultimately all atheism in 40k becomes is "I really hate my dad for taking me to church, I'd never do that to my kids and would never ever tell them what to think" and then a surprise pikachu when the kids start turning to fundie christianity or worshipping trees. Or the Emperor and Chaos in this case.
If the Space Marines practiced some sort of secular civil religion that defined their overall culture, I wouldn't have this complaint.