Growing shallots can be a learning experience. You can cut the flowers off the scapes but the stem can continue to grow... What I do is to wait for the scapes to grow about two feet and cut them off for cooking... The bulbs with scapes wont store well and can be tough but I learned to leave those in the ground to continue grow and eventually the scape slowly gets pushed out to the side of the plants...

They are about 2 feet high now. I will go cut them off before they bloom.