It's a loss in the short term, but a good idea in the long run. It's not that they are losing money (really think about how wealthy amazon is, three million dollars is nothing to them), it's that that people will come back to them.
I think the album costing that much was a good idea, even Lady Gaga thinks it's a good idea. It's getting the music out there to the masses for a very reasonable price. Isn't that the intention?
The record label should not have been charging Amazon that much for a sale. That's crap. As much as I dislike Gaga, what she said is pretty true. However, she should not have been making more than 99cents off those sales and yet it seems she did.