A few comments and clarifications:
I think it would be more fair if you titled the question "what should we do when a user uses an answer for commenting?", or "should we allow low rep users to use answers for commenting?".
This is not a change, AFAIR, we were (at least I was) doing this even before becoming a moderator. We were posting similar comments on such answers which were should be comments but were posted as answers.
The FAQ says that:
Answers that do not fundamentally answer the question may be removed. Answers that are …
- commentary on the question or other answers
- asking another, different question
- “thanks!” or “me too!” responses
- exact duplicates of other answers
- not even a partial answer to the actual question
… may be be removed.
The comments are just explaining why the answer is removed, and it is more respectful to user than just removing their answer without any feedback. (But it seems that explaining thing can cause more problems than not explaining them. :)
Now regarding the question: "Should we allow low rep users to use comments or should we discourage them?"
I don't have a strong feeling about forbidding them, and I don't have a problem with exceptions (e.g. the comment is too long to be posted as a comment, which I think we can think of them as partial answers) but here are some points that I think we should take into consideration:
This is circumventing the SE system, and I don't think it is a good thing to do unless there is very good reason and strong need for it.
You are right that moderators can turn answers into comments, and I try to do this, but I would prefer if this does not become a norm, i.e. users posting comments as answers, then they get flagged by users for being not an answer (not even a partial one), and finally moderators turning them into comments. I think it will be too much work for moderators if low rep users start to comment in this way. Too much moderator intervention.
I was one of the people who have complained about the restriction previously, and don't think SE has a very good reasons for the restriction. But based on our experience so far, this restriction has not become a serious issue (I haven't seen anyone complain about this in recent months). My explanation is that those users who become part of the community easily gain the required 50 rep points by posting one or two answers, we get quite a number of question each day and expecting users to answer one or two question before being able to comment is not a strong requirement. So in practice the restriction is not as serious as it might seem at first. In other words, I also don't think there is a serious need for allowing low rep users to comment using answers.
Just to clarify another point, I think there are legitimate cases where a user can use an answer to post a comment, e.g. the comment is too long for a comment. (I am also personally OK with any comment that is adding some new information in the direction of finding an answer, I consider them partial answers.)
And there are other cases where it is not legitimate (IMHO) like a one line question about the question.
I understand that the problem might be the following: my comment might mean to some users that answers should not be used as all to comment, where the FAQ entry only say that they may be removed. So I think there might be a better way like posting a better comment that would not imply that commenting using answers is totally forbidden. (Or maybe I shouldn't post any comments at all regarding use of answers for commenting, that might end up being a better option.)