Complex sentence: Another interpretation is that Dylan, as a jab at critics claiming subtle drug references in rock music of the time, wrote a song that seemed to clearly be about drugs, but was actually about the civil rights movement.
Split into simpler sentences: Another interpretation is that Dylan wrote this song as a jab at critics claiming subtle drug references in rock music of the time. He instead wrote a song that seemed to clearly be about drugs, while it was actually about the civil rights movement.