retract = strikethrough + disable voting
delete = make invisible (a second step after retraction)
The comment was retracted before receiving any votes, with the purpose of being visible but not subject to karma (visible here). I am surprised that this was not clear from the quote; perhaps it's a matter of giving the benefit of the doubt to the user vs the moderator? It was deleted by a moderator, not the user. I think this deletion is very clearly the right action, to the point that I'm surprised that VN didn't delete it when he left his reply.
If you want to avoid clutter, you should delete, not just retract, but it looks to me that you do. If you change your mind, you should say that, not (just) retract, and probably not delete. The main point of retraction is to let someone pull out of the karma system without disrupting a conversation. In principle, an edit saying that should discourage downvotes, but in practice it doesn't. Also, for good or for ill, it discourages reading the comment a bit more than an edit.
I consider the main point of retraction to be a reconsideration of the value of a comment - that is, it should be used to say "This is, on further consideration, wrong, or without value" while leaving the reasoning for why it was wrong (or without value) in the first place intact, so other people don't commit the same mistake. This is so regardless of whether the karma value of the comment is positive or negative.
Karma values are, in general, a useful gauge, but not an ultimate gauge, of the usefulness of a comment; they are in the end the consensus view of a post or comment, which may or may not be "correct".
http://www.quickmeme.com/Overcoming-bias-guy/popular/1/?upcoming