Actually Star Wars will still win after the flood is released. In just the clone wars alone (which was just 3 short years compared to the entirety of the Star Wars timeline) over a QUINTILLION battle droids were produced and deployed. They were meant to swarm their enemies and crush what little tactical advantage they had. Just do that to the flood. They are very very immune to the effects of the flood after all. And without taking out the head, they can always just relay the message back to command and seeing how they are robots, they can scan the flood and find out any biological weaknesses in them.