The interaction between the electric dipole moment of a trapped molecular ion and the configuration of the confined Coulomb crystal couples the orientation of the molecule to its motion. We consider the practical feasibility of harnessing this interaction to initialize, process, and read out quantum information encoded in molecular ion qubits without optically illuminating the molecules. We present two schemes wherein a molecular ion can be entangled with a co-trapped atomic ion qubit, providing, among other things, a means for molecular state preparation and measurement. We also show that virtual phonon exchange can significantly boost range of the intermolecular dipole-dipole interaction, allowing strong coupling between widely-separated molecular ion qubits.