My concern about encouraging the use of HTML comments is that they might end up being used as a kind of "secondary talk", hidden from observers, and only noticed by people actively editing an article.
There are a lot of times when I'm puzzling over an edit war, but I almost never edit in those cases, because of my political position around here. If people start leaving comments like
<!-- YOUR MOTHER SUCKS DUCKS IF YOU CHANGE THIS PART -->
that's not good. :-)
--Jimbo