Female rabbits are renowned for being moody sods. getting her spayed will stop the moodiness, but may not stop the thumping which could be due to her being scared by something. Alternatively you will just have to get used to the thumping. My old rabbit used to launch herself at your arm when you tried to clean her out, she had a male (neutered companion, which she frequently tried to mate with - her doing the 'humping' of his head) I think its just a female thing. The anesthetic for small animals is much less risky now, but if you find that she resigns herself eventually to being petted after the grunting, launching and eventual sinking of teeth in to flesh can you deal with that?
But in all honesty there is no hard and fast rule about behaviour of female rabbits, spaying her might calm her 'tude, but then again it might not. Don't you know some women who are moody ALL the time?