I deleted a comment on that question recently due to it being non-constructive criticism.
I delete comments all the time, some are flagged, most are not. It is part of the duties of moderation. The goal is to focus the site on awesome answers to great questions. People should not have to read and understand a bunch of comments to get to the meat of the answer. This is the primary difference between SE and forums in my mind.
Comments are ephemeral on this (indeed all) SE sites. You should have no expectation of them lasting forevermore. This has been stated quite clearly by Jeff Atwood, founder of StackExchange:
not every user-generated byte committed to memory is sacred. Particularly in comments, which are meant to be lightweight and ephemeral. If you want to post content more likely to survive, do it in an answer.. this is 100% [status-bydesign]... – Jeff Atwood♦ Feb 12 '10 at 21:43
Also see Robert Cartaino's response (Director of Community Development)
Comments are designed to be second class.
And from Shog9 (Community Coordinator)
Comments are - at best - second-class citizens on SE sites. The primary goal is to generate a repository of good questions and helpful answers, not lengthy back-and-forth discussions.
In general, I'll let comments live for 30 days. After that they are prone to get considered for deletion when I see them. If there is useful content in them that contributes to the question/answer, I'll leave them or roll them in (ideally this is an ongoing process).
Update in response to comments
Note that I used, "In general" and "considered for deletion" Despite comments to the contrary, I do not blanket delete all comments. I feel that the vast majority of deleted comments any reasonable person would agree are not useful. Examples "+1 I agree" or my favorite: "Did you mean XX?"/"Yes"/"You should edit that in"/"Thanks, I just did"/"Great". My deleted comment count can really climb when I see one of those!
Moderator is a weighty title, in reality, Janitor fits better. I spent a lot of time editing or removing comments/answers/questions from the site that I feel most people would not find useful.
Will some people consider some deleted comments useful? Sure, I am a semi-sentient bag of water and other people may have a different subjective opinion on various matters.
Since the original poster is not defending the deleted comment in question, I'd rather debate openly any other example of a deleted comment that someone feels was really adding to the discussion.