Start with the fact that floods do, in fact, kill people all the time, and that nature is in God’s hands in some meaningful sense (unless you don’t believe that Jesus actually stilled the Sea of Galilee). I would argue that nature is not yet where God intends it to end up, and that sin has something to do with the past and present vulnerability of earthly creatures to suffering and death in all kinds of ways–including floods.
All people who have died in floods and other natural disasters have suffered because of God’s judgment on human sin. Jesus died so that such deaths need not be the end of the story for anyone, and God’s mercy will prevail in ways we can only dimly glimpse. But judgment on sin as a concept and a reality cannot be excised from the Bible without tearing loose a lot of muscle, and even an artery or two, if you know what I mean. Jesus himself issues a lot of dire warnings in the gospels.
Noah’s flood seems to be based on an old Mesopotamian story, which might go back to the experience of an actual Mesopotamian family. If that story has been told in hyperbolic terms to embody some universal spiritual truths, well, welcome to the world of the Hebrew Bible. Colossians 1:23 says the gospel in the first century was peached to “all creation under heaven,” so there’s a touch of that expansive tendency even in the New Testament.
As for genocide and general brutality in the early stories, it is the equivalent in historical narrative of self-mutilation and cannibalism in the ethical teachings of Jesus. Jesus throws those brutal, shocking images out there–without further explanation–and invites his listeners to grapple with them to find the message they are conveying. Likewise, the narrative carnage of OT conquests is there to underscore God’s condemnation of certain cultural practices he wanted his people to avoid.
One approach in teaching is just to read the accounts and let listeners grapple with them, and go into more detail for those who approach with questions. However, sometimes even that strategy is not practical. I wish I had easy answers for those situations.
Studying the Bible with serious intent is not for the faint of heart, and many would, understandably, prefer to skim the surface of the thornier parts and move on. Those who are willing to wrestle with the text will have the experience of Jacob with the angel; they will emerge blessed, though not unscathed.