To their credit, all of the bookstores described in the article are fighting it, including Amazon and Borders, on grounds that release of that information would have a chilling effect on free speech. The big ones, at least, have the money to pay for a serious legal team without thinking too hard; smaller independant bookstores are more vulnerable to pressure, and have been subjected to raids with no apparent purpose other than intimidation.
This sort of privacy issue has gotten national attention before --- when Bork's video rentals came up at his confirmation hearings, the upshot was a bill which protected the confidentiality of video store customer records. I guess they thought it just couldn't ever be a problem with bookshops.
In the meantime, while patronizing my excellent local bookstores, I stay out of their frequent buyer databases --- and pay cash.