Clarification on ALL points
First, the reason apple "refunded" you $1399 even though they don't have proof (they never saw your receipt) that you spent $1399 is a complete coincidence. When the Rev Bs first hit Apple Stores, they were selling brand new Rev As for $1399 to clear stock; saw them with my own eyes. It turns out that B and H was selling them for the same price Apple was. The point is, this is a legitimate Apple price point.
If you buy a shirt from GAP for $20 and bring it back without a receipt after it's been on sale for $10, they're only going to give you $10 credit.
Second, they screwed up by not offering you the option to have your Rev A repaired or replaced... as has been pointed out, they have lots of refurbs of this model.
Third, you screwed up by taking the offer. You should have first demanded that they give you the Rev B for nothing, and when that didn't work you should have demanded repair/replacement of your Rev A. They didn't do what they should've done, but they didn't con you, or twist your arm either.
Fourth, it's odd that everyone you talked to acknowledged the superiority of the Rev B. We all know that better CPU+faster RAM+better GPU+bigger HD = better designed MBA, but Apple hasn't ever acknowledged the problems with Rev A. In your case they have tacitly done so. Unfortunately, they're using it to your disadvantage. But, in their defense, these problems are precisely why you were able to save money on the computer in the first place.
Fifth, I find it odd that they didn't just give you the Rev B for free. I took my Rev A (paid $1150 at MacMall AFTER Apple was selling it for $1399) in and complained of overheating. I was straight with them and told them that I didn't think there was anything "wrong" with it, meaning I didn't think it was broken. I told them, "everybody knows the Rev A was poorly designed" and the Genius actually acknowledged that fact. When they ran the tests (the tests that your Rev A failed) it passes with flying colors, but it got REALLY hot during testing so they replaced it.
This just goes to show you how much of this stuff depends on manager's prerogative. My manager felt like being cool, yours felt like making money. I don't know that either of them followed SOP.
I truly hope you get your money back. Be persistent, assertive, and NICE. At the very least I suspect you'll get $400 "worth" of Apple gear.