I don't believe they will, and here is why:
This is not a dollars-and-cents business decision, in my opinion. This is completely about image. If Apple sells Microsoft Windows in their store, they're essentially saying:
Look, we're buddy-buddy! One and the same. We're merging. It's a marriage of Mac OS and Windows. We're all together now. Together. Where your Windows viruses can destroy your Mac documents! Forget all those years of rivalry and what you saw on "Pirates of Silicon Valley" -- we're friends! GOOD friends. Bill comes over and ****s my sister on the weekends, et cetera et cetera ad nauseum.
It's selling out (in image, at least) all Mac zealots. It clotheslines the idea that OS X and the software constructed for it is sufficient for 90% of all users. It anally rapes the intelligent shopper's perception of the company's confidence in its product! Imagine going into Taco Bell and seeing a new Burrito Exquisito on the menu. They've pulled out all the stops advertising for this thing: Celebrity testimonials, flashing lights, talking dogs, et cetera. In fine print: "also comes with 1 hard taco, 1 soft taco, and 1 burrito of your choice, of equal or lesser value." And when you ask why, they say "well, you might not actually like it, so here's a bunch of stuff that you'll probably like."
It's ridiculous. It makes little (if any) sense. Why in the hell would you ask someone to buy a product that they are ostensibly embittered with, infuriated with, that they have supposedly lost work and hours of productivity to? When you go to the Hospital, do they have plates full of rat poison for you to snort?
I honestly can't buy this idea. There are too many scenarios in which Apple loses. And it wins how? By robbing Circuit City of that $5/unit? By fulfilling some imaginary agreement? ****, Apple doesn't sell Linux or NetBSD! I am printing on a printer that works with OS X, but is not sold in an Apple store!
All in all, it just doesn't make sense to me. Not because of dollars-and-cents directly, but because of how it would affect Apple's image. I can see them licensing Microsoft's APIs and making a better DarWINE, but I can't see them selling a packaged vanilla Windows OS. It'd blow my freaking mind. And if it happens, I will personally stand on IJ Reilly's shoulders and publicly eat my own pancreas.