That's a cool idea. It would be interesting to have a situation where the evil organization, be it Quantum or Spectre or the Guild of Calamitous Intent or whoever, suddenly has to put the kibosh on a fellow supervillain because he's just too crazy and threatens to queer the pitch. So they reach out to Bond, the only man they can really trust, and give him the resources to eliminate the threat. Suddenly Bond is being escorted around by waxy-skinned Russian guys in matching jumpsuits; he can whip out a phone and call in a helicopter attack whenever he wants; he's even given access to a Ken Adam set and a chifforobe full of Mao suits. Or something like that. Anyway, Bond is effectively an honorary villain for the duration of the film. Could be a recipe for silly excess, or it could be a fun, genre-bending way to end Craig's era.
I must admit I wasn't so much thinking of Bond as an honorary villain as the crime syndicate realising they had seriously miscalculated - they hadn't checked the resume of the mad scientist they had hired for their "pay up or else" plan. It could either work as an alliance similar to TSWLM without the "loved me" element, or Bond tackling the villain, stopping his insane scheme, only for the villain's backers to turn up and reveal that they had been secretly nudging 007 in the right direction all along - not for altruistic reasons but because a secret global crime syndicate can't hold to ransom a world that no longer exists.