Isn't one of the "10 commandments" - "Thou Shalt Not Kill"?

Perhaps you don't understand the rules. The commandment would be better understood as "thou shalt not murder." Read the condition of those who were destroyed in the flood and the numerous warnings they were given of an impending destruction if they did not repent. You will find that the flood had nothing to do with murder. It had to do with the cleansing of the earth of those who refused to listen to the warnings of their impending destruction if they did not change their evil ways.