The <!-- --> tags are standard HTML (comments) and with the exception of being used for browser compatibility hacks, should normally be innocuous. Of course they appear when the source is viewed, so I could understand why you might want to remove them in some cases.
Unfortunately, I don't know of any filter in apache to remove them. Since they are valid HTML, they will be parsed and sent to the browser.
The easiest way I can think of to remove them all from a set of html files would be to use sed with a regular expression that searches for the tags and removes everything in between and then replaces it with an empty string.