There was a story mission in 1.0 that tied into them. After completing the quest, we got a ring with our deity on it. We had to travel on a pilgrimage to all the gods to pray for Bahamut wouldn't go "RAWR BOOM!" Got our ring when we reached our stone.
Well it's good that they at least attempted to tie something tangible with them.
I doubt they would scrap that, SE loves that kind of thing, and making us speculate on what influence it might have over your character.
Plus it's one more thing to agonize when making your character.
Hopefully they perks are something cool if it is still in 2.0 and not something too arbitrary. If they are going to want to go the route of WoW with balancing for PvP then they might end up fairly useless. That or they may do like GW2 did with racial bonuses and disable them for pvp or at least make them only useful in PvE.