The ride will not be shutdown, but you are right concerning whether the ride is at fault or not. All of the serious related injuries and unfortunate deaths have not been the cause of the ride, but then again, DCA's rollercoaster lost brake control and injured over a dozen people. To this day its still in operation with long lines.
A park ride, especially one outside of the box, is like any other major investment: you take a risk, build it, and then you open it and see what happens. The ride itself is a huge success, and Disney will continue to make changes it deems necessary to improve the experience.
People have to remember that ANYTHING can happen on any ride. Would Disney permanently shutdown Space Mountain if someone were injured? Would they permanently shutdown Spaceship Earth because someone decided to try and pass a small child from one car to the other, and yes, that has happened. A young boy died from a heart defect on Rock n' Rollercoaster, and its still hugely popular. A man died on Splash Mountain after being hit by a vehicle, and its still open and widely popular. All of these are equal in comparison to what has happened on Mission: Space, and I'm starting to see that people are putting it in a category of its own only because of their own fear of an attraction where the sense of control is far less than any of the other examples above.
All I'm looking for is perspective. The same people who say this ride needs to be shutdown and they would never ride it are the same people who get in their cars everyday and whether they want to admit it or not, put themselves at risk each and every time they turn the key.
This stuff happens. Its part of life, and its far better to enjoy it than to live in a bubble.