That's mainly due to the normalization of the molecular orbitals.
The bonding/non-bonding orbitals are normalized as [itex]\psi_\pm=\frac{1}{\sqrt{2}(1\pm S)}(\phi_A\pm \phi_B)[/itex] where [itex]S=\langle B|A \rangle[/itex] where the plus sign refers to bonding and the minus sign to the anti-bonding orbital.
With the exchange energy [itex]H_{AB}=\langle B|H|A\rangle[/itex] the bonding energies are approximately [itex]E_\pm\approx \pm H_{AB}/(1\pm S)[/itex]. Now with 1-S being much smaller than 1+S, the anti-bond is more destabilzed than the bond is stabilized.