Applying fading to all the comments just because a downvoted comment has a parent that happens to be at the top, seems wrong.
I've lost count of how many times I've seen perfectly good insightful comments around here that get ignored because some people decided to downvote them for some arbitrary reason. In fact, it's so bad, that I'd say I've barely seen any good instances of fading for the past year; they just seems to encourage group-think almost every time.
I'm ok with the idea of downvoting meaning disagreement, since that's how voting systems always end up being used anyway (not to mention pg approves of that interpretation as well), but penalizing comments to become practically non-existent based on a few downvotes (last time I noticed, a score of -1 started the fading) is just not conducive to interesting discussion.
So perhaps a margin of, say, five or six downvotes should be necessary before any visual effect takes place. Not only would this no longer bias readers against a comment before having read it, but it would guarantee that the faded comments more accurately reflect the standards of the community as a whole.
Another approach is simply to hide the offensive comment and weight the entire thread in relation to other threads when determining display order.