That premise is alright as long as the pilots obey the restrictions. What happens if a terrorist takes the plane right into downtown? Not much time to stop him from doing his dirty deed. Not that I'm defending Daley by any means.
For single-engine aircraft that don't want to go beyond gliding distance of shore, the coast of Lake Michigan represents a major flight corridor. Meigs Field or no, there will be many aircraft which have good reason to fly near the city. Even if the lake shore flight corridor were closed down (unlikely) it wouldn't take long for a plane apparently headed to Midway to change course for some terrorist action.
Of course, I don't think the airplanes that used Meigs Field would have posed much of a threat to the Sears Tower anyway, but that's another story.