We show that the valence electrons of Ba3NaRu2O9, which has a quasi-molecular structure, completely crystallize below 210 K. Using an extended Hubbard model, we show that the charge ordering instability results from long-range Coulomb interactions. However, orbital ordering, metal-metal bonding and formation of a partial spin gap enforce the magnitude of the charge separation. The striped charge order and frustrated hcp lattice of Ru2O9 dimers lead to competition with a quasi-degenerate charge-melted phase under photo-excitation at low temperature. Our results establish a broad class of simple metal oxides as models for emergent phenomena at the border between the molecular and solid states.