It's actually pretty typical for coups/mutinies.
Your position is challenged by military brass, so you imprison/execute them. Anyone charismatic enough to take you on is going to have been popular with the soldiers, so now a heavily-armed mob with tanks and artillery is pissed at you. Now you have two problems, with only two solutions-- eat some shit and hope to make peace, or die.
Putin played it safe in flipping the script-- negotiate surrender, appear to resolve the dispute peacefully, then stage an "accident" of the rabblerouser once tensions are lower. Cooler heads always prevail.