You cant close that option, but rebels are highly unlikely as this was the largest military planet of the UNSC. It would be really difficult for them to get there and to stay hidden. At this part of the UNSC-Covenant war most of the inserructionist planets and bases had been wiped out and I'm quite sure that Humans where; at least to some stage, allied against the Covenant.
There might be more creatures like the flood, or something that the Forerunners left by?