Well, you can set affinity, but then you'd get the problem you outlined. So you could multithread.
But I see two inevitable problems if you get this working.
Disk I/O will slow horribly when you've got threads running in parallel.
And when it's trying to run more trivial tasks, the cost of getting other cores to work at them may actually be negated.
Although this is true of any concurrency. The fact minecraft doesn't even have an actual engine, and just tacks things on to the architecture will just make CreeperHost cry.
I wish I could be of some help, but I do not know how to computer enough.