Bleeding Kansas refers to a series of violent conflicts within the Kansas Territory and neighboring cities near the Missouri Border. Since this conflict took place prior to the formation of the Confederacy, it’s a bit of a misnomer to ask who the military leader of the south was. Also, there wasn’t a single, consolidated command structure to the two sides in Bleeding Kansas, so asking who the overall pro-slavery commander was is also a bit inaccurate.
There were however some notable figures in the fighting that could be considered "command figures" similar to the role John Brown played. Henry C. Pate, who would eventually become a Confederate commander, was captured by John Brown and his men at the Battle of Black Jack while commanding 22 pro-slavery fighters. John W. Reid was the leader of a 250-man force at the Battle of Osawtomie where John Brown again led the anti-slavery forces to victory. This was the largest Bleeding Kansas fight prior to the Civil War.
Brown was also not an official Union commander. He and his sons led several sorties against pro-slavery forces, but the fighting was very disorganized. Mobs of men known as “Boarder Ruffians” fought with anti-slavery “Free Soilers” without much military discipline or official support. The position of the U.S. government was to stop the killing all together.