I agree with James Forrester that this should be done in stages, and that the first stage would be to "show comments and let them be deleted.

In terms of isolating hidden (aka "invisible") comments, the logic is pretty much the same as for templates, except easier: look for <!-- as the left boundary, then look for --> as the right boundary. Treat the result as a block that can be deleted or moved.

Looking at https://en.wikipedia.org/wiki/Help:Hidden_text , it's not clear that text within an invisible comment is essentially nowikied, but that is in fact the case, because - by definition - the text can't be seen in either read or preview mode. From a programming viewpoint, this means that even if, for example, there is an http link within the comment, or a reference - both quite possible - no rendering is needed: all text should be treated as text, NOT interpreted.

What the person doing the edit sees is really the critical question. It seems to me that there are two options:

(1) Display as a text, mixed in with regular text, but in a different color font and background color. This is what is done with templates. Regarding the color: Hidden comments are typically warnings/notices to editors, so perhaps yellow? The font/coloring will, ideally, make it clear that the text is not part of the article. 

(2) Treat like a comment in Excel - put a character (I suggested a warning icon - see http://findicons.com/search/warning; in yellow) into the visible text that, when a person hovers on the icon, displays the hidden/invisible text. While this is less visible to editors, in some sense - they have to hover to read - it's more visible in the sense that hidden comments, in wikitext editing mode, are in the same font as everything else, and thus less likely to be noticed than a bright yellow warning icon.

Option (2) lends itself nicely to the second phase mentioned by James: Here there would be an icon on the toolbar, for adding a new comment. In addition, if a person hovers over an existing comment, then an editing icon appears nearby, which allows the person to edit the comment or to delete it [via trashcan icon].