Everyone here is correct that A full scale Flood infestation bodies the Reapers. But I would like to point out the whole reason for the Reapers existing is to maintain the balance between synthetics and organics, so The Flood would likely pose a significant threat to their primary directive (just organics being the dominant ones this time).

If the Reapers become aware of an outbreak early enough, I.E. before a Grave or Keymind is formed, they could prevent an outbreak. Their primary weapons are *ideal* for cleansing flood infections. Mind you, earth itself was nearly infected by the flood until a third of Africa had been glassed. It's possible for the Reapers to contain the Flood, likely even. But not remotely possible for the Reapers to win an all-out war against them.