When you remove an electron from F2, you remove it from an anti bonding molecular orbital, not a bonding molecular orbital. Hence, BO=0.5(8-5)=3/2, which is a higher bond order, (which is obvious when you consider the lower occupancy of anti bonding energy levels) and a shorter bond length. Remember; you remove electrons from the highest energy level first, and anti bonding orbitals are the highest energy levels.