I'm no expert on Forerunner anything by any means, but shouldn't that work, at least in theory? The Composer more or less destroys select organic matter and collects the thoughts and memories of its victims, which are then converted into data. So with that in mind, couldn't the Composer have been set to target, say, Flood biomass? And once said biomass has been composed, wouldn't it be possible to just destroy the resulting data? Boom! Flood menace ended, Forerunners survive.