Is there any reason why these stores need to store the full magnetic stipe details of the card in the first place?
To make a charge, the POS terminal packages the mag stripe data (and the encrypted PIN-block if doing debit) together with the POS terminal's ID, the amount to be charged, and maybe the CVV2 or the billing zip code, etc., into an HTTPS request to the payment processor. A second or two later, the payment processor responds, and the terminal completes the transaction.
If that's how Target's POS terminals work, then the hackers probably managed to push a "software update" out to the terminals causing them to tee the data off to the hackers' server whenever a transaction was made.
The reason the debit PINs were safe is that the PIN pads on which the customers enter their PINs are separate self-contained devices which encrypt the PINs before they leave the pad. Only the payment processor has the key needed to decrypt the PIN blocks, and PIN pads don't accept "software updates". PIN pads have been hacked in the past, but such attacks are far less scalable because they require modifying hardware at each affected POS terminal.
The new news about Target breaching contact info for 70m customers simply confirms that the hackers had free reign on Target's corporate network.
But in order to pull it off on the scale they did, the bad guys must have broken into Target's corporate network. Apparently, the level of access they achieved allowed them to raid the marketing database as well as to hack large numbers of POS terminals to leak the card swipe data.
The marketing database, BTW, contained name and contact information, but not credit card details. The bad guys might find it useful for phishing attacks.