Okay, I find the rather interesting. The "Atheism Is Dead" blog claims to "promote intellectual responsibility" and reverse the effects of "manipulative attempts of atheist apologists." But the particular style they have for moderating comments looks quite manipulative. I will present my argument and let the reader decide.
First off, I fully understand that they have a troll trying to disrupt the site. They have every reason to use moderation to block the troll. I do not object to that. I am, in fact, in full support of that part. The objection is a little subtler.
When they approve comments, they do not approve them in the same order as they were written. Comments which are deleted for cause are not relevant to this. So if they get comments A, B, C, D, E, F, G, and H, all acceptable to the moderation policy, but comment C is inconvenient to them -- say it makes a point they would rather not address -- they are apt to approve A, B, D, E, F, G, and H at once, wait 12 hours, and then approve C. When C is approved, it shows up buried.
When someone objects that a legitimate comment has been deleted, they are certainly able to point out that it does appear in the thread. But people reading the discusstion on the blog are likely to miss the comment. If they come back to the blog after having previously read through comment H, they are likely to pick up where they left off. They have no reason to believe that an unread comment now appears between B and D, which they have already read.
A user with a username of Scott complained about the "out of turn" approval of the comments; and the blog moderators acted as though it was a complaint about the fact that the blog was moderated at all. Either they are oblivious to the actual nature of the complaint (which I doubt as I added a comment to clarify -- I don't expect it to be approved) or they are doing this deliberately to manipulate what people see. This is a subtler tactic that has the same effect as deleting comments except when someone is actively checking whether a comment has been deleted.