Isn’t half of an atom an explosion?
Usually it is referred to as an ion. Depending on what atom you start with.
Half an atom might be, more likely it is an ion. However 2 atoms half an Ångström apart are probably OK.
In short you would be closing the distance between the outer shells of the atoms and not splitting the atoms itself, as the riddle states that the distance between the engineer and the woman would halved so they would almost be touching, not the distance between the centers of the two, where they would occupy the same space.