Admittedly that would be a concern, the Japanese who knew that it was far too late to run away from the Red Army's advance or were already encircled did take it out on the civilian population (there's actually a Chinese film about this, which includes scenes of Type-95's going up against T-34's) however the focus was also on getting away as quickly as possible if they still could (one of the major causes of death on the Japanese side was wounded soldiers being abandoned) combined with the complete collapse of their supply chain, and command being beheaded with the Soviet capture of the Kwantung High Command at Hsinking, the capacity for mass atrocities would be greatly reduced with Mao increasing his control of the countryside and the Red Army and the KMT rapidly liberating the cities and ports.
No matter how quickly the campaign went, there would still be more casualties than OTL. There's also the possibility of CCP/KMT issues breaking out in areas where they run into each other.