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Do you have to treat it? I imagine that the current latrines are pit latrines, which would get flooded out anyway so downstream water is already contaminated? The priority would be treating the water to make it safe for drinking.
Putting that to one side, are you looking at buying a completed system, or making something? Separating the solids from liquids would mean less storage required, a pivoting shelf in a plastic bucket can be used. Also a friend is currently testing these in India, https://www.usaid.gov/div/portfolio/bvv-tiger and it would be fairly easy to fit a plastic drum with some. The issue would be getting worms when the flood has started, but if the cesspits already have them you have a head start.