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Or just straight up bury the tribal goddess.

Sounds about right

I completely agree with you there should be more contact for the tribal people in general like event for joining them and following their religion or the complete opposite convincing them that she is no god 

Yeah having a quest like that kinda works with how mysterious the wastes really are if at one point you could revive her or at least wake her up, then it's up to the player on what they do with this "goddess" even though she is most likely part of an experiment pre-war