I stand to be corrected, but I believe you may be liable for stamp duty anyway. The exemption you refer to applies in the case of marriages and civil partnerships, but not siblings, I believe. I hope I'm wrong.
But if I'm not, the amount owed would be based on the value of what you are buying and not the amount of outstanding mortgage. So if the property is worth £250k and you are buying his 50% share, your liability to SDLT would run to the £125k you would be paying him.
In that situation, you would be exempt. If the share you are buying is under £250k, you would be liable to 1% stamp duty. You (and your girlfriend) would only be liable to pay 3% if the share of the property you are buying is, say £550k and your 50% share is £275k.
Hope that makes sense. If I'm right, you might want to talk to an accountant about the possibility of buying a smaller share of the property that keeps you under the 1% SDLT charge level - and then buy another slice a bit further down the line. That's possible with shared ownership schemes and might apply here...
Anyway, the number to ring is 0845 603 0135. Come back and let us know what they say as I'd be interested to know myself.