1. A method for controlling a joint in a medical robotic system in response to user manipulation of a master input device, comprising: computing a distance from a sliding surface using at least a position error associated with commanded movement of the joint; computing a reaching law gain as a function of the absolute value of the distance; computing a current state for an integrator using a prior state of the integrator and the distance; computing a product of the reaching law gain and the distance; limiting the product to be less than a maximum control action; modifying the current state of the integrator using the limited product so as to limit a sum of the product and the current state of the integrator to be less than the maximum control action; computing a sliding mode control action by summing the product and the modified current state of the integrator, and processing the sliding mode control action to generate one or more command signals to drive the joint according to the user manipulation of the master input device.