LLVM isn't really a VM, it's just a compiler toolkit. And really, the overhead of converting your data structure to LLVM IR is almost certainly trivial compared with the cost of the optimizations it is performing.
LLVM IR is definitionally coding to a virtual machine. It doesn't bear a ton of similarity to the underlying architecture in most cases. gcc's GIMPLE is the same idea. (That it's compiled down to machine code doesn't make what you're working with not-a-virtual-machine.)
Heh, I originally wrote something more pedantic then edited it down. It's definitely a virtual machine insofar as its an abstract computational machine, but it's not in the probably more common definition of "an interpreter, possibly with a JITing compiler on the side, for an abstract computational machine" (though LLVM does have an interpreter, it's not really ever intended to be used for anything).
