For what it's worth, I'd be interested looking into other alternative search solutions in the future (such as Lucene). The search engine in IPB is abstracted to the point where we can accomplish this in the future should there be a good enough reason.
I think, though, that anyone interested in replacing their search engine would be happy enough with Sphinx anyways, so it's probably better to spend our resources on improving Sphinx than providing alternatives.
Unfortunately, as Charles said, there's only so much that can be done about MySQL...