How can absolute binding free energies be calculated?
Free energies are computed by transforming one state into another, e.g. by transforming ligand A into a ligand B (inside a protein in our case). This transformation yields the difference in binding free energies between ligands A and B: $\Delta \Delta G^{bind}_{A \rightarrow B}$. This is a relative binding free energy.

On the other hand, if ligand A is transformed into nothing, it's absolute binding free energy is calculated: $ \Delta G^{bind}_A$. 

In both cases ($\Delta G$ and $\Delta \Delta G$), we are calculating differences between two states, and never calculating the absolute free energy $G$ of a single state. This is probably what you meant by: "only relative free energies can be calculated."

PS: since binding occurs in a solvent, it would be necessary to take ligand solvation and protein solvation into account, in order to properly describe the unbound state. For example, in the calculation of $\Delta G^{bind}_A$ described above, ligand A should appear in bulk water instead of disappearing completely.