Photoionization of an atom in the presence of a neighboring atom of different species is studied. The latter first undergoes resonant photoexcitation, leading to an autoionizing state of the diatomic system. Afterwards, the excitation energy is transferred radiationlessly via a two-center Auger process to the other atom, causing its ionization. Assuming a fixed internuclear distance, it has been predicted theoretically that this indirect ionization pathway can strongly dominate over the direct photoionization. Here, we extend the theory of resonant two-center photoionization by including the nuclear motion in van-der-Waals molecules. An analytical formula is derived reflecting the influence of molecular vibrational dynamics on the relative strength of the two-center channel. For the specific example of Li-He dimers we show that the two-center autoionizing resonances are split by the nuclear motion into multiplets, with the resonance lines reaching a comparable level of enhancement over direct photoionization as is obtained in a model based on spatially fixed nuclei.