"Help, help! I'm being oppressed!"
Honestly, how is it focusing on the oppression of a culture to keep them from founding an organized religion? If a people never had an organized, centralized religion, what have they lost? And if they got along just fine with what in real life amounts to a pantheon why would they need a central religion?
Particularly if they receive bonuses to their pantheon, this wouldn't be removing an option from a player for no reason - it would be rather nicely representing the way of life of that people. I do think that the Aboriginals would need a defense against Missionaries though, since they will not have Inquisitors available. Perhaps a Shaman unit that drains one spread religion use per turn spent next to a Missionary of another religion?
While I don't know much about Aboriginal religion, I do know they had nothing remotely resembling an organized religion, not even much continuity of beliefs from tribe to tribe. If your people's "religion" is a collection of superstitions and spirit-calling witch-doctoring, I don't really think you have anything to evangelize to other people or any reason to stamp out new beliefs among your own people - which is what Civ5's religion gives you.
And, I'm sorry if I misunderstood, but: did you say CL would be treating the spirituality of a minority people as primitive? Might that be because... Aboriginals were pretty darn primitive as long as they were left to their own devices? Why is calling a primitive people primitive an insult? It's not like we're calling them apes...