The colonel suggests it, but March is forced into applying for a transfer to the superintendent of contraband. Why?

The colonel suggests that March transfer orders when March is angered that the soldiers receive nothing but a slap on the wrist because of his complaint. The colonel tries to convince March that it is nothing personal, but when March begins recounting his years of service, the colonel snaps that Dr. McKillop discovered March in the passionate embrace of a slave, leaving March dumbfounded.