I think it's because the gnomes are not as nice as they seem to be.
Think about it, why are they really there?
Runepowder. What are they going to do with runepowder? Blow people up in Baldur's Gate. What can that stuff really do? According to Philomeen, a small amount of it can blow up an entire city. What does she have? An entire powder keg of it. She tells you right out that they all came there for that stuff, and Wulbren knows the formula. That's why he was taken to Moonrise, so the Absolute could extract it from him.
So, I'm thinking that they're not exactly so nice. I could see them turning on you at the drop of a hat.
