I had a small video on my channel a while ago which originally procured a few thousand hits but when someone made a much more popular video response (made popular due to virality through reddit/digg) my viewings for that video shot up due to, as you described, "reverse click-through".

Yeah, is it any surprise that the click-through rate would be abysmal? People want to watch the video, not responses to the video. But as you say, when you are on the response, you may actually want to watch the original video and so the reverse click-through rate should be much higher.