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Correct. Halos were holding pens for Flood, and their purpose was to eliminate the possibility of the Flood exponentially growing again.
If the Forerunner took the time to eliminate all the other hosts from the galaxy, then why would they be so careless as to let their guard down? They should have left for a Shield World or wherever the rest of the Forerunner went. The Sentinels were there to control outbreaks, but they obviously failed.
I think that some of them could be Forerunner Flood, but I think most of the extra Sangheili and Human forms were added in because it was needed in the game.