Since the growth of GaN using molecular beam epitaxy (MBE) occurs under metastable growth conditions, activated nitrogen is required to drive the forward synthesis reaction. In the process of exciting the nitrogen using a plasma or ion-beam source, species with large kinetic energies are generated. Impingement on the growth surface by these species can result in subsurface damage to the growing film, as well as an enhancement of the reverse decomposition reaction rate. In this study, we investigate the effect of the kinetic energy of the impinging nitrogen ions during growth on the resulting optical and structural properties of GaN films. Strong band-edge photoluminescence and cathodoluminescence are found when a kinetic energy of ~10 eV are used, while luminescence is not detectable when the kinetic energies exceeds 18 eV. Also, we find that the use of conductive SiC substrates results in more homogeneous luminescence than the use of insulating sapphire substrates. This is attributed to sample surface charging in the case of sapphire substrates and subsequent variation in the incident ion flux and kinetic energy across the growth surface.This study clearly shows that the quality of GaN films grown by MBE are presently limited by damage from the impingement of high energy species on the growth surface.