By means of N-body simulations we study the ion and electron dynamics in molecular first-row hydride clusters when exposed to intense and short X-ray pulses. We find that, for a particular range of X-ray intensities, fast protons are ejected from the system on a considerably shorter time scale than that of the screened core. As a consequence, the structure of heavy atoms is kept intact", which may be relevant in the context of X-ray based molecular imaging. Moreover the final charge states of the heavy ions are considerably lower than those of the ions in pristine atomic clusters exposed to the same laser pulses, which is in agreement with recent measurement of methane cluster at the LCLS in Stanford.