Computer security was broken during the Viet Nam conflict, as there were systems that had to accommodate multiple classification levels at the same time, and they couldn't do it with the OSs of the day. Multilevel security was developed after that, which leads to Capability Based Security.
Essentially, your current OS requires you to have absolute faith in any software that runs on your behalf. If it goes rogue, or gets confused, almost anything you could do to sabotage yourself... it can do in milliseconds.
On the other hand, if the OS didn't have that requirement, and instead let you choose what files to open, and enforced your decisions, you wouldn't have to trust your software at all.
From the point of a GUI user, they wouldn't see any difference in behavior. File Open still works like always, but the logic behind the scenes is slightly different.
Command line usage, that's a tougher nut to crack. There needs to be a standard way of defining what files you're passing on the command line.
We could stop blaming everything but the OS... but we likely won't. 8(