What I don't see being addressed is the fact that, at the end of the day, Apple is at fault here.
When Apple approved the application to the store, (as far as I know) they knew about the $999 price tag. By letting it in, they are saying: "Ok, you pass." Regardless of what people are saying about Apple being 'understaffed' or lax about the approval process of applications, it was still allowed onto the store. The application had no malicious intent, didn't do anything funky, like porn, and was just a regular app, that being said an expensive one.
I believe Apple is at fault for this. If Apple hadn't allowed the application to be added to the store, then they wouldn't have to worry about refunding the money to the 'accidental' purchasers. That would be like me customizing my dream computer on Apple.com or whatever, and accidentally pressing order. "He said it was an accident, so let's believe him."
Apple should refund the purchasers who asked for a refund, but only because it was their fault to begin with. But, the developer should receive full payment, regardless of those two refunds. He made an app. Apple let it on. Apple decided not to implement any warning features to the store, and thus, let this happen to themselves. The accidental purchasers also have a nice $999 application for free now, too.
Apple should also bring it back to the store. As I said above, their was no malicious intent, and nothing against the Store policy as far as I know. They really need to get their act together soon.