It very much looks like a situation in which the system has already been compromised and is running malicious programs that it shouldn't. These malicious programs could still face the hurdle of being held at bay by the permission system that prevents them from reading your key file.

However, they could indeed be able to circumvent the permission system by figuring out what sensitive data your program left behind in uninitialized memory and in CPU registers.

Not leaving traces behind then becomes a serious issue. Could the kernel be tasked with clearing registers and clearing re-assigned memory before giving these resources to another program? The kernel knows exactly when he is doing that, no?

It would be a better solution than trying to fix all possible compilers and scripting engines in use. Fixing these tools smells like picking the wrong level to solve this problem ...