That's the thing: It would be some nice twist if the navi cleans out the WG from within, but I very much doubt that happens.
Basically any shonen manga with some mysterious "overlord king" like Imu will always let that main evil force get destroyed by the protagonist - the SHs/Luffy.
I'm pretty sure that if Oda really writes a plot where Akainu & Co. try to overthrow Imu & the Gorosei, they actually get their butts handed to them. There is a reason those dudes were able to rule and enslave the world for 900 years.
Yeah, I think there will be some trade off, in which the marines accomplish more independence while not diminishing Imu's role. Because for now, as mighty as Imu might be, things seem to get out of hand, with or without his permission. But given the scene with him cutting up wanted posters, it seems he is legitimately feeling threatened, and the WG is also not able to stop events from happening. Urging their agents to kill Luffy and abduct Robin, ending up awakening Nika and not getting their hands on Robin, unable to stop the likes of Morgans publishing information they don't want to be published.
Also, given how anxious they behave in front of Yonko interactions; be it one of the Gorosei turning pale as Shanks contacts Whitebeard or the other Gorosei being afraid of what could happen if they anger Kaido, it does seem to me that the WG keeps its control due to a multitude of things, some of which being keeping a power structure alive that is barely questioned (we know this from real life politics, where politics themselves have a power structure under their command) combined with propaganda, which is part of keeping the power structure alive; deliberately trying to erase information that might make them look bad or would allow the general public to get the bigger picture. On the other hand, large parts of the new world and the strongest islands are not under the WG's control, they are or were under the control of pirates. With the Gorosei admitting that Wano is still unconquerable to them, acting on Doflamingo's behalf since he knows their secrets and even failing to assassinate him while he is under Magellan's protection in Impel Down. Doesn't sound to me like a very encompassing power.
But I'm looking forward to how Oda will handle that.