Yes I see your dilemma. Beans don't like to be checked in their growth and pulling this one at this stage with very little root established will be quite a shock; in fact if you were to germinate another seed the new one might easily catch up with a shocked bean messed with.
I see a few alternatives: first you could let the bean roots fill the pot and move it up to more soil when you can extract the root ball intact, or let the bean grow and then when the pot is filled and roots come out of the drain hole stand the whole thing on another pot full of soil to allow the roots to continue expanding, or let it be as is and start another to grow alongside in its own pot with generous soil.
My second suggestion makes me uneasy since you have the bean in a nice clay pot and balancing that on top of loose soil is inviting the loss of a good pot. My inclination would be my third alternative.