The problem and major plot hole with that theory stems from how cryosleep functions. Anyone exiting cryosleep would have been an easy target for the Flood. You see, people in cryosleep are generally naked, as wearing clothes can cause some very serious freezer burn. Also, after exiting cryosleep, crew members would have been slightly disoriented for a short time. In conclusion, the Flood would have wiped out most of the crew immediately.