The growth of smooth superconducting MgB2 films in a non-epitaxial regime is challenging. Here, we study the formation of superconducting MgB2 films by solid-phase reactive inter-diffusion of sputter-deposited Mg/B multilayers, employing ion beam mixing to disperse the multilayers prior to thermal annealing. The multilayers are intermixed by room-Temperature bombardment with 500 keV Xe ions to doses up to 4 × 1016 cm-2, followed by thermal annealing to form MgB2. Results show that such an intermixing step leads to a dramatic reduction in surface roughness of superconducting films. However, lattice defects produced by ion bombardment reduce the critical superconducting transition temperature, an effect which scales monotonically with ion dose. The critical temperature can be recovered by an additional defect annealing step at.