tl;dr: Automatic bad ends for athiests makes morality system impotent/unimportant.
I would've hoped that "being atheist" in PF wouldn't mirror the D&D mythos in terms of afterlife, but it appears I am wrong.
http://forgottenrealms.wikia.com/wiki/Wall_of_the_Faithless
Because honestly, these constructs for atheists makes morality worthless, as you ultimately aren't judged on your deeds, but rather who you worship in terms of getting an afterlife.
Basically, this construct reduces morality to a question of belief or non-belief from the beginning. If you believe, then you go to the god you believe in and they do what they want with you according to whatever rules/laws/tenets they put in place (which are ultimately arbitrary per god). If you don't, you get shoved in a box and then into the belly of something else to be consumed (if my understanding of the other respondents to this topic are saying is the official campaign setting of PF).
This, imho, devalues the whole "belief in a deity" because you are putting a choice of worship vs ultimate annihilation for each soul above what they achieved in the world (Good or Evil). Many mortals will "hedge" their bets and go with worshiping something. But then is that true belief, or just paying lip service to a system in order to avoid a worse fate? if it is just lip service, is that sufficient for a god to accept someone into their "afterlife"? if so, then why bother having the alignment stuff at all? if not, then that moon must get a lot of soul-snacks...