J. Otto Pohl, author of Ethnic Cleansing in the USSR, 1937-1949, left an interesting comment offering explanations for the deportation of the Soviet Koreans from the Far East.
[T]he deportation of the Koreans had to do with several reasons. One underlying reason that fed the others was that like all other extra-territorial nationalities there national construction took place outside the territory of the USSR. Hence Moscow could not fully shape the national history of the group to create a fully Soviet Korean nationality the way the Soviet government could with native nationalities. They would always maintain an outside essence that could not be trusted near the borders of the Soviet Union particularly near their ancestral homeland.
Second, there was the issue of land conflict between Koreans and Slavs in the Far East that had existed since Tsarist times. Land conflicts throughout the USSR became intensified on a national level during the 1920s and 30s. In Kazakhstan and the Caucasus this led to the expulsion of Russians by natives. See Terry Martin's an Affirmative Action Empire for on how this worked in Asian ares of the USSR.
Finally, the issue of espionage which was the official rationale for deportation. It is true that the Koreans in the USSR were not well disposed to the Japanese. But, they were well disposed to fellow Koreans. It was feared that this fraternal kinship would lead them to shelter ethnic Koreans sent from Korea by the Japanese to act as spies and diversionsits in the Far East. Frequent crossborder traffic by Koreans and families with members on both sides of the USSR-Manchurian border intnesified this fear. The fact is that Koreans in the USSR could harbor pro-Japanese Koreans infiltrated into the area without knowing it. By as it were draining this sea of support by creating a completely White Soviet Far East, the Soviet government made such infiltration impossible. Any Asian caught in the Soviet Far East after the deportation of the Koreans and Chinese would just be assumed to be a Japanese spy.
There is also the issue of having harmed some Koreans that of all of them might become hostile to Soviet power. Hence the original deportation order which only covered the border regions was later expanded to include all of the USSR east of Lake Baikal. By sending the entire population to Kazakhstan and Uzbekistan the NKVD made sure that no potential threat could develop among the population.