In organic photovoltaic (PV) cells, the well-established donor-acceptor (D/A) concept enabling photo-induced charge transfer between two partners with suitable energy level alignment has proven extremely successful. Nevertheless, the introduction of such a heterojunction is accompanied with additional energy losses as compared to an inorganic homojunction cell, owing to the presence of a charge-transfer (CT) state at the D/A interface. Based on the principle of detailed balance, a modified Shockley-Queisser theory is developed including the essential effects of interfacial CT states, that allows for a quantitative assessment of the thermodynamic efficiency limits of molecular D/A solar cells. Key parameters, apart from the optical gap of the absorber material, entering the model are the energy (ECT) and relative absorption strength (αCT) of the CT state. It is demonstrated how the open-circuit voltage (VOC) and thus the power conversion efficiency are affected by different parameter values. Furthermore, it is shown that temperature dependent device characteristics can serve to determine the CT energy, and thus the upper limit of VOC for a given D/A combination, as well as to quantify non-radiative recombination losses. The model is applied to diindenoperylene (DIP)-based photovoltaic devices, with open-circuit voltages between 0.9 and 1.4 V, depending on the partner, that have recently been reported.