Tracking position and orientation independently affords more agile maneuver for over-actuated multirotor Unmanned Aerial Vehicles (UAVs) while introducing undesired downwash effects; downwash flows generated by thrust generators may counteract others due to close proximity, which significantly threatens the stability of the platform. The complexity of modeling aerodynamic airflow challenges control algorithms from properly compensating for such a side effect. Leveraging the input redundancies in over-actuated UAVs, we tackle this issue with a novel control allocation framework that considers downwash effects and explores the entire allocation space for an optimal solution. This optimal solution avoids downwash effects while providing high thrust efficiency within the hardware constraints. To the best of our knowledge, ours is the first formal derivation to investigate the downwash effects on over-actuated UAVs. We verify our framework on different hardware configurations in both simulation and experiment.