"An intentional walk with the bases empty? This is baseball, not backgammon!"
Also, the catcher is not completely defenseless - he is an armored tank on much of his body and if he does not have the ball and is worried about his safety (ie being blindsided), then he should not be in the baseline.
He has equipment on but as the rules are he has to block the plate and hold onto the ball. The catcher is going to get hurt far more often than a runner ever will. The nail rarely hurts the hammer. I think we have all seen runners primarily focused on hitting the catcher and making him drop the ball and not focused much at all on touching home plate. I think we have all seen elbows and forearms to heads, necks, and chests of catchers.
That rule is an anomoly in what is in essence a non contact sport and its probably time it is removed.
I am not sure what you mean by the catcher not being in the baseline. If you mean if he doesnt want to get hit then he should give up the run - then I dont agree with that. If you mean he can stand off to the side and try to tag the runner out as he runs by, thats fine as long as they are strict in calling the runner out if he runs out of the base path to avoid the tag. That also assumes the catcher has the ball long enough to move into a better position, thats not always the case.