Bond tendered his resignation but that doesn't mean it couldn't be reversed. It also doesn't mean he couldn't be "useful" to them in "another" way. His mind doesn't get wiped clean as soon as he hits <send> on his lap top in the Gulf Of Venice.
If you assume that the 'organization' would simply take its lumps and 'let it go' or "cut its losses", then i've got an ocean-front condo in Nevada for sale (on-line only) for you.
But that doesn't alter the fact that Bond had killed everyone- Vesper was free to go. They couldn't get her even if she hadn't committed suicide.
Perhaps the Quantum people in the UK like Mitchell could have taken her later- but why would Vesper suspect that? She didn't even know Yusef was Quantum- she had no idea of the size of it. Also, why was Vesper the only one they could kidnap? Why not take M's mysterious husband? Bond's aunty or someone? Seduce Bond with a female version of Yusef? Why does Vesper killing herself mean that they have no way of 'getting to' Bond if they're so powerful? They appear to have 'let it go' or 'cut their losses' there.
Plus, even if somehow they had got hold of Vesper, M knew full well that Bond was off sailing with her- would she really not have suspected anything if he'd just simply said 'oh sorry; didn't mean to resign. Gone off Vesper now'? He would have been an immediate security risk if Vesper had suspiciously disappeared.
It kind of works, but think about it any further (as it asks you to) and it falls apart somewhat.