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No, you are right, Halo doesn't kill Flood, it kills their food.
This is what I thought when I played Halo 3:
There was only one lot of Flood that ever escaped the places that they were trapped on. In Halo 2, the Flood used the In Amber Clad to escape off Delta Halo into High Charity. They then used High Charity to leave Halo altogether.
So now, the Flood were either trapped on some Forerunner structure or flying through space in High Charity. But the Gravemind sent a ship from High Charity to Earth. So now they were in three places: Forerunner structures, High Charity and Earth.
Rtas 'Vadumee glassed the entire surface of where the Flood had spread on Earth. So now all the Flood on Earth were dead.
Once again all the Flood were either stuck on some Forerunner structure on flying in High Charity.
High Charity then moved to ther Ark. Now the Ark was located just outside the galaxy, whereas the Halos were located within it. So by activating the Halo at the Ark, and not activating the other Halos, they would eliminate all the 'local' Flood without killing everything within the galaxy. I don't particularly understand that, however, the Ark ended up being destroyed and therefore so did the Flood at the Ark and High Charity. So I guess all of the free Flood ended up dying.