So, let me clarify something. Jinbe's position in the crew is still left uncertain, right? I notice many forum-goers are still debating what he'll be doing on the ship. One suggestion is as a guide, another is as an "ambassador" among pirates, a third is simply as "fishman" (AKA lifeguard/fisherman/wtf?)…
You know what, get rid of that last one. It's stupid to think that the crew needs a lifeguard. The other two are viable options, though.
Hm, following the thought of Jinbe becoming an "ambassador"; just how much use would that be for the crew? It's important to know how politics among both the government and major pirate powers work, but this position is not something Jinbe would always be, nor is he such a specialist. That leaves the other option: guide.
But, what kind of guide? Certainly, Luffy wouldn't want someone like a tour guide, and I highly doubt Jinbe has sailed every corner of the New World (surpassing Roger's climactic journey, heh). If Jinbe does have some knowledge about certain countries, i.e. how they interact with the WG, it would definitely prove useful. But, that would imply he is no stranger there. The SHs, even with whatever info Nami and Robin have gathered, are still very much in the dark about that ocean. Having to rely on only one member to safely traverse the perils... Hell no! This isn't supposed to be safe passage; it's an exciting adventure into the unknown! Okay, scratch that. No guide... but he can at least give some advice before they go.
But, what to do about Jinbe? And I doubt the prisons will be enough to hold 100,000 NFP + Hody's gang... Oh, how's this? Neptune minds getting those prisoners back to Impel Down or somewhere, keeping Hody's gang under close leash (as having a former army agent in prison may bring suspicion), giving the WG the impression that Ryuuguu Kingdom, is still loyal to the WG but is also strong enough to mind itself. And Jinbe finally can go into peaceful retirement (possibly in the Fishman Dojo). As to where his fellows from the Sun Pirates have gone, the crew may meet them sooner or later. This sounds like fanfiction, but there's the plausibility.
Besides, why would one of Luffy's major allies and mentors join as an underling? Vivi had no choice at the time, so she doesn't count.