Enhanced coherence in HoW10 molecular spin qubits has been demonstrated by use of clock-transitions (CTs). More recently it was shown that, while operating at the CTs, it was possible to use an electrical field to selectively address HoW10 molecules pointing in a given direction, within a crystal that contains two kinds of identical but inversion-related molecules. Herein we theoretically explore the possibility of employing the electric field to effect entangling two-qubit quantum gates within a 2-qubit Hilbert space resulting from dipolar coupling of two CT-protected HoW10 molecules in a diluted crystal. We estimate the thermal evolution of T1, T2, find that CTs are also optimal operating points from the point of view of phonons, and lay out how to combine a sequence of microwave and electric field pulses to achieve coherent control within a switchable two-qubit operating space between symmetric and asymmetric qubit states that are protected both from spin-bath and from phonon-bath decoherence. This two-qubit gate approach presents an elegant correspondence between physical stimuli and logical operations, meanwhile avoiding any spontaneous unitary evolution of the qubit states. Finally, we found a highly protected 1-qubit subspace resulting from the interaction between two clock molecules.