Hi ShaneC,
I can answer your question as I am in the same situation as yourself and find it very frustrating!
You will have to pay stamp duty as your gf is not a first time buyer for stamp duty purposes. She can still claim mortgage interest relief for the 7 years allowed and you can also claim interest relief from the date ye buy your house.
We are struggling to save a deposit + stamp duty as my bf is paying half of a mortgage on a house that he cannot sell or rent for reasons I won't get into here.
Good luck with it all!!