I don't know the director's intentions, but I couldn't help seeing the Kotov character in this very fine movie as a stand-in for the real-life figure of Marshall Mikhail Tukhachevsky - in which case, his status as a popular war hero is the answer to your (OP's) question.
Because Stalin saw his fame and popularity as a threat and/or affront to himself, and NKVD chief Iezhov was able to manipulate his fears to get rid of probably the best Red Army commander; indeed, of most of the best Soviet commanders. IIRC, of the 15 men who held the highest army rank of Marshall, 13, including Tukhachevsky, were executed in the course of Stalin's 1937 purge of the Red Army.
Like the fictitious Kotov (who would surely not have remained just a colonel), Tukhachevsky was the most celebrated Red Army commander during the 1918-1921 Civil War; he was arrested by Iezhov/Stalin and shot (in 1937, not 1936), but "rehabilitated" after Stalin's death; his wife died in the GULag and his young daughter was also imprisoned, but survived.
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