I was involved in this. First, let me illustrate the situation by a rough analogy. Second, I will explain in detail what precisely happened, as it is slightly complex due to the set being new. Finally, some more commentary.
An imaginary situation
Suppose somebody asks:
'How do I deal with a group size of 150 students in a calculus course?'
Then somebody comments:
'Why not teach in smaller groups?'
To me this comment feels unnecessary. While it is far from offensive or anything like this, it does not really add much, does not answer or clarify the question, yet somebody might get annoyed. Or even if not somebdoy just might reply something, perhaps even agreeing, and somebody else joins in and so on creating 'noise'. And, if one really wanted to know if splitting the group could be an option or why things are as they are one could and should ask directly.
This is an example of a comment that in is 'not constructive'; this is a reason to flag, and then they are reviewed and possibly removed by moderators. At least this is commmon practice on many sites (though not on all, see below).
The reason for deleting comments in the present case was also mainly just this, nothing dramatic, merely standard general clean-up. Now the details.
The rough timeline
Some comments on the thread got flagged, but only as 'not constructive' (see Can we be respectful? for context and public source).
Robert Cartaino thus 'sweeps away' almost all comments on question as a quick routine procedure very common on some SE sites and explains he did so. [Note we had no moderators for the site then.]
I notice that this cleaning even affected a reply to the two remaining comments, and ask Rober Cartaino to restore this. This did not happen; I stronlgy assumed simply because he likely gets 1001 notifications all the time.
The sites gets moderators (including me).
I protect the question. I notice there are some more flags on comments on answers. I handle them via deletion, and explain in a comment on Can we be respectful? why I did this.
I undelete the comment I wanted undeleted. Answer questions by Saint George, clean up some of my comments and move on. (Or rather I think I undeleted afterwards as I had an issue with the interface at first.)
Some comments Let me first recap the reason for my deletions.
It was first of all for consistent handling of flags on this one thread and, second, since I am of the opinion the comments were actually not constructive, being somewhere between off-topic in the sense of unrelated and rhetorical/provocative.
Yet, I admit I would have (personally) preferred we had had a collective discussion about how much comment deletion we want in general before that (since different sites have very different standards and this already frequently caused hard feelings on various sites). Still I felt we should finish this one thread in a consistent way. (Also these deletions would be reversible.)
To give an actual example (I hope noone minds this being reposted, let me know if you feel differently): On Ken W. Smith answer you commented
Aren't we going to talk about atheist mathematicians such as Russell, Clifford, Erdős, Markov, Tarski, and Zariski? Russell, for example, was known for the "Russell's teapot" argument for atheism.
This is somewhat like my example. It is rhetorical, and feels somewhere between unrelated and unfocused. And, even, contrary to what you assert I do consider this as rather to the chatty end; you ask a question that feels designed to produce a reaction (and to start a conversation). What is the actual point you want to make?
Do you think it would be a better idea to achieve the given goal there to mention them? Do you think readers are unaware of the existence of atheist mathematicians and need to be informed about this? Do you consider it as genuinely/in all contexts problematic to only mention 'one side of it'?
Each of this might even be legitimate (though perhaps not all necessary). Yet if you really feel the need to point out one or all of these or still something else, I think you should be direct and not rhetorical regarding what you mean. (Now, on meta, you were more direct. I think had you said just this, in a slightly nicer tone, the comments would still be around.)
Moreover, I think on this site (I think I would have another opinion for other sites) it will be a good idea to have the policy of not questioning the details of context that is sketched in questions too much, especially not if it is presented in a rather neutral way and is rather out of control of OP, as in the present case. (Sure, there can be exceptions, but generally speaking. Conversely, I also would not want people using the context to promote some view too much, thus the restriction to neutral. But I think this 'neutral' was the case here.)
I hope this clears up the situation a bit. But I feel there is/will be more need for discussion to figure out on which "style" we want to settle.