You can already make Linux run any binary you want for the same CPU architecture, for example, wine uses this functionality. You can make it run natively binaries from other architectures with a rewriting VM like qemu (although I'm not sure qemu itself can port binaries between architectures, just that it's rewriting VM). Your VM can enforce security with a sandbox instead of a hypervisor, like the Java, C#, node ones do.

Hypervisor is not the standard, it's one of the many ways people do it right now.