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Aokiji and Smoker have long been established their disturbance with the chain-of-command, as have other people such as Garp and Sengoku. I don't think the WG will fall per se since the alternative is the world succumbing to the Yonkou. Probably after the Gorosei fall Aokiji and Smoker assume leadership and give the WG its long overdue political reforms.
One Piece is about ever evolving factions. The revolutionaries and the arms race being run by Donflamingo are two sides of the same coin. That story is just starting to get revealed. Coby and Helmeppo will be Garp's Marine legacy and rise up the Marineford ranks honorably. Mirroring Luffy's fame. Smoker and Tashigi will continue with G5 as ostensibly hunting Luffy and rooting out nefarious elements against justice. Smoker will try every encounter to actively arrest him, but each meeting will also make Luffy a hero that they will let go because their intervention was a net positive. They are characters that are testing Luffy to see if he will slip from his path. They take the place of Luffy's mentors (Garp, Dragon, Shanks) who cannot interact directly. Aokijiki will not join Luffy but interact with the revolutionaries in the future. Lending aid where necessary.
I think sengoku quit the marines because he was feeling older and older.... with the end of the war came about the beginning of a new era so he so fit for someone else to lead the marines into the new era. I don't think the coverups would be enough to make sengoku quit. If such a thing was an issue then he wouldn't have been a marine to begin with. As head of the marines it is likely that he himself would have already been involved in many shadier things than that directly or indirectly...
Anyways, as for smoker and aokiji joining the strawhats... my guess is a plain no. Aokiji and smoker are men of principle, they fight for what they believe in. The strawhats are not like that, they are going on for their selfish desires. The world government is their enemy but only because they mess with them. If the world government had not actually persecuted the strawhats then the strawhats would not even bother with giving them a look. I think eventually they will fight alongside them but not with them per say much like smoker has done against crocodile and ceasar. At best I would argue that aokiji and smoker will end up with the revolutionaries although the revolutionaries are not necessarily pro pirate. They want to destroy the world government and make them pay for their crimes, they want a new world order. In that light perhaps pirates and specially the yonko are in the long term enemies of the revolutionaries as once they win (if they win) it is them who are going to have to keep pirates in control.