The God of the Gaps is the essence of Irreducible Complexity. Once science discovers how the IC mechanism could indeed have evolved (or discovers how it did evolve), then it's no longer IC. By definition.
And if you want to argue that ALS doesn't think the Designer of the flagellum is God, good luck.
Well whether ALS does or does not believe the designer is God, I do believe it. In any case, my comment was addressed to your argument. A false one. As to whether God created evil, I think I have displayed the answer clearly.