if it were my bike, yeah, remove the entire cable and shoot it good with some quality lube. you dont want to push any water or crap back into the primary when over-lubing it to clean it out.
if you have a service manual, it describes how to remove/install the cable. its pretty easy to figure out on the S, but one HUGE word of caution... when you get the cable free from all its mounts (lever, wire guide and clamp) make sure you dont put extra stress on the cable where it enters the side case.
when unscrewing the cable from the case, keep the cable completely straight, as if it were a solid rod. install it in this same fashion and keep the torque on it VERY low. a lot of people have snapped or stripped threads removing/installing the clutch cable. i think its because its hard to keep straight and doesnt need much torque to seat it. ive removed and installed the clutch cable a few times without any issue whatsoever.
as for the 'packed grease' comment, ive just heard of people filling that area with some thick grease to help keep water out. sealing the top portion of the boot and checking often after wash/rain rides has kept mine fine. just another way to combat water getting in there by adding some thick grease. up to you though.