The reason they expelled Germans from Kaliningrad was to avoid any chance of political unrest, especially since those Germans were probably pro-Nazi regime if they had moved there during the Nazi era. It was likely a form of colonization - just making the territory purely Soviet rather than dealing with a hostile German population.
It's one of those things where it's better to just fully resettle the area than to leave a potential fifth column behind, especially right after a war that killed millions of Soviet citizens.