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I figured out a hack to do this, which is to set the desired joints for the controller on the parameter server and then unload and reload the controller.

rosparam set r_arm_controller/joints "[r_wrist_flex_joint, r_wrist_roll_joint]"

rosrun pr2_controller_manager pr2_controller_manager stop r_arm_controller

rosrun pr2_controller_manager pr2_controller_manager unload r_arm_controller

rosrun pr2_controller_manager pr2_controller_manager load r_arm_controller

rosrun pr2_controller_manager pr2_controller_manager start r_arm_controller

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