Maybe it should be printed on the main download page:
Note: Please read the readme file included in the package. This does not install like a standalone WordPress site.
Or something like that.
Then, they can't say they didn't know because it's right in front of their face when they download it?
I dunno. No matter what you do, or so it seems, you aren't going to weed them all out and get them to rtfm.
We had the same problem on my last project. The readme file was very good, and most read it. Problem is, they'd skim through it, and not follow it to a T. Then wonder why their site didn't work. It wasn't difficult to accomplish and install, but it was more than click-type-click.
MU, at least at this point, just isn't for a less knowledgeable user that has trouble with html and css, let alone php. But then again, it's not really geared towards them like it's big brother either. At least that's the way I see it.