The only answer is security, these deaths, though unfortunate, are not numerous enough to even warrant looking at an alternative design for the landing gear bays. These are what would be termed acceptable losses.
As is usual in all aircraft incidents it comes down to the engineers who are to blame or who have to find a solution (Lockerbie, "Why aren't planes made bomb proof!"). Let's remove the undercarriage all together and have them land on a trolley attached to a conveyor belt, there wouldn't be any wheel wells for anyone to climb into and the amount of weight saving would be great. These issues lie with security.