I'm afraid that they will have to pay the extra stamp duty. If the wife's old PPR is sold within 18 months of the purchase of the new PPR, they may be able to claim a refund of the extra SDLT.
As you will read in Section 2.4 here, a married couple are treated as one unit for the purposes of the extra stamp duty and so buying the property in one name only won't help.
I hope this clarifies things for you but let me know if you have any further questions.
My apologies. I was looking at the 16 March 2016 document.
Osborne caved in yet again on another policy killing its intended effect which was designed to help people onto the property market in the March Budget, as you can read here.