Considering a Mech Marine is bigger then a tall tree, I fail to see how the Flood could be a problem...And with it being a robot, it couldnt really be converted...
Yeah, the civ population would get infected and turn into the army, yada yada, but as I remember from SupCom, the civ population is very small.
And Plus...I mean cmon, one cerberus would be enough to hold the line from thousands of flood.