You are focusing on the why-God-destroyed-the-world part. The opening post question is why a flood? Couldn't God have snapped His Fingers and popped all the evildoers out of existence?
Although I think the original post was looking for a modern theological explanation, I think an ancient theological explanation makes more sense, and is more interesting.
When the earliest versions of the flood myth were written, nobody had yet imagined omnipotence, and the Jews/Hebrews still had a pantheon of multiple non-omnipotent gods, just like everybody else around did. Along with true omnipotence and monotheism, another concept they either hadn't yet thought of or at least hadn't yet incorporated into their myths/religion was utter nothingness, and with it the modern absolute sense of creation (something from nothing) or destruction (something into nothing). That's why the closest they had to a creation story, like all others, actually started with something, which one or more gods would merely tinker with and rearrange: in their case, a great abyss of water.
So their story of the destruction of the world would naturally take the form of whatever was the greatest form of destruction that they did have a concept for, converting the world into the closest thing their mythology had to a concept of nothing: just a great sea. The Babylonian version of the flood story makes the equivalence between the flooded world and the primordial abyssal sea pretty straightforward in a couple of ways. First, Ut-Napishtim must destroy his home in order to use the materials to build the ship, which makes the ship the direct replacement for everything he has, his personal little world. Then, the description of the ship's design is equal in length and width (more like the disk-shaped rendering of the world than the shape of a boat) and directly compares its roof to the sky (which they thought of back then as a solid dome over the world, holding back the water outside it). Ut-Napishtim isn't putting things from this world in storage to bring back out later; he's recreating a small version of the world to replace the one that's getting destroyed.
The Hebrew version doesn't include some of those little details, but does add something else that still indicates a reason why the world's destruction would be in the form of a great storm instead of, for example, fire or plague or plain old personal violence against everybody: the choice of which god did the destroying. In both versions, it's done by the warrior-god, the guy who represents the imposition of one group's will on another by force (Enlil/Yahweh). But Yahweh also had a specific association with destructive storms, such as in a treaty between two Semitic-language-speaking kings in which Yahweh was invoked to enforce the treaty by destroying either side's ships & docks with waves & wind if they violated it. If the Semitic deity of choice to wipe us out had been Anat, for example, then the mechanism would have been running around personally pulling our guts out and rolling our heads down the streets instead of a flood.