The first part of what I suggested, a windowed VM, is pretty easy to do. You could do it with a bit of script hacking and a copy of RPCEmu. Basically, whenever the filer (any OS) runs a RISC OS executable, it uses a script to launch RPCEmu with a modified boot sequence so that some parameters specifying which program to run can be passed along to it. Obviously, as someone else pointed out, it's not much use for an OS like RO as drag and drop, but it would work.
Making it seamless is the hard part but not insurmountable. Surely, this is what Aemulator is doing? Once that was running you could abandon legacy compatibility and start integrating something like WIMP2.
The other point that I was making was that a module that allowed programmers to run a piece of code on the second core would probably quite useful. Making RO a multithreaded, multi processor OS seems like too much work. I'm sure that most users would be prefer video acceleration for example.