The atomistic Segregation-Charge Transfer (SCT) model is adopted to analyse the nucleation of crystalline or amorphous phases in irradiated binary compound thin films, both metallic and non-metallic. Dense collision cascades, which result from ion bombardment, lead to the formation of liquefied droplets of matter, each surrounded by the crystalline matrix. The space and time evolution of a prototypical cascade involve non-equilibrium compositional and electronic density profiles at the cascade- crystalline matrix interface. This occurs because one of film components preferentially migrates to such interface, which is thus enriched in it. System relaxation to metastable equilibrium is simulated by local charge transfer reactions (CTR), each involving a pair of dissimilar atoms of the initial compound, that make up a dimer of an effective compound. Three quantities are calculated in the framework of SCT model, namely the energy cost to introduce an effective compound dimer into the matrix, the difference of formation enthalpy between each couple of corresponding effective and initial compounds and the local deformation the film undergoes as a consequence of ion formation by a CTR. Threshold values are found for the above structure stability parameters that provide physical interpretation of the apparent separation between amorphised and crystalline compounds, both metallic and non-metallic.