Actually, it's good writing. Story 101 drama trumps logic. The Audience will overlook minor illogical choices if it helps to craft a good story which this did. I mean going with your sentiment why doesn't Magneto just toss Wolverine a few blocks every time they meet? Or why doesn't Charles find every supervillain on Earth using Cerebro and put them to sleep and tell the Avengers, Fantastic Four, FBI, CIA, Interpool, Scotland Yard etc where to find the evil sleeping beauties so they can be taken in? Wouldn't this foster into good will towards mutants? Well, he doesn't do it because no Supervillains kills the drama for the Marvel Universe.