There is an interesting degree of independence. A lot of Java semantics is not baked into the JVM, and in the case of invokedynamic there was for a time a significant JVM feature that java didn't use.
The JVM is a pretty decent target for languages with garbage collection, objects (of some form), and methods / functions. Those facilities are useful for most languages these days, and provide a large degree of interoperability. I don't have to really thing about ruby calling java and back again, no calling conventions or issues with garbage.
It will be interesting to see whether WASM will support those kinds of features.
Using the Java language on other VMs confuses people in exactly the same way that using the Java Virtual Machine for other languages confuses people.
The outcome might have been different had they called it something like HLVM instead of JVM.
It's much better to build this in layers - a standardized lowest layer that's something like WASM, then a standardized object model on top of that etc. That way, you can have a single stack supporting a broad variety of languages, with degree of interop compatibility dictated by how much in common they have.
As for LLVM, sandboxing has never been a core feature (AFAIK).
WebAssembly only exists because Mozilla went with asm.js instead.