One thing I don't get from your story: in what sense was this guy "helpless"?
If I were living in the D&D world, I'd have no problems with this: I would know that there's no binding capable of holding a competent character, who may have stilled, silent spells available, or who may be Houdini's protege. However, I would also know that nobody in the world can escape from being unconscious. If I have a villain in my clutches, and the villain is likely to hurt other people if he escapes, I have a duty to ensure he doesn't escape; sometimes, knocking him unconscious is the most humane means to accomplish this duty.
Ironically, another means of subduing villains without killing them--poison use--is also considered less humane by many players and DMs than the use of lethal force.
That said, perhaps you could've describe the unarmed attacks in less brutal-sounding terms. I suspect the hotbutton issue you hit for the bard's player was modern-day police brutality, which often (and dramatically) takes the form of kicking helpless suspects; the bard's player did NOT want to identify with those images.
Daniel