Yep, if you both buy a 2nd hand house, Stamp Duty applies.
I've heard of a few couples who have purchased a house in similar circumstances (one FTB, one not) and NOT paid Stamp Duty. They mess around with names on deeds and mortgages but as far as I can see this is totally illegal and they're opening up a whole world of pain if/when Revenue come chasing them down the line.
See
[broken link removed]
particularly sections 5, 7 and 9.
As the previous poster said, you would still be entitled to the full FTB mortgage interest relief.