Linux is the best operating system for a project like this. The system call binary interface is stable at the processor architecture level:

https://www.kernel.org/doc/Documentation/ABI/stable/syscalls

http://man7.org/linux/man-pages/man2/syscalls.2.html

http://man7.org/linux/man-pages/man2/syscall.2.html

Any Linux process can perform Linux system calls, no matter what language the software is written in. Instead of relying on C libraries to do everything, a compiler could emit system call code when necessary. The entire Linux user space could be rewritten in a higher level language that way. Rust would be the likely candidate but there's no reason a Lisp or Scheme couldn't do it. The language would need full support for features of binary interfaces such as function calling conventions, pointers, structures with padding and alignment, etc.