Reviewing through your description, I would like to clarify the behavior you are seeing as comments should not appear in the "view as PDF" option. For example:
1. I created a document with a couple of comments:
2. Used the "view as PDF" option found in the actions dropdown:
However, replies (found in discussions) will appear in the "view as PDF" feature.
If you are referring to the behavior seen with replies to discussions, there is not currently a way to disable this in the out of the box product, however, I would recommend submitting an idea to the Ideas for Jive space (if you do not yet have access to this space you can request it via - Are you a customer? Request customer-only access today ) if you are interested in seeing this feature added to a future release.