The Engineers missed their mission date 2000 years ago, when human technology was not very advanced. He's awakened, on a military base, on his ship, by an intruding force obviously of a technology far advanced from the one he was getting ready to go wipe out on Earth at the start of the common era.
A military man's only prudent action would be to strike first in an attempt to neutralize the alien, in this case human, threat.