I suspect a lot of people read in batches. They take a break and read a dozen new stories over the course of a few minutes. If the exclusion is site wide, and the endorsement rate does not turn out as high as you hope, that would in effect in many cases mean that they only get one comment per batch. If there are more than one story they want to comment in on a batch, they will need to remember to go back during another break and revisit the old story.
2) Won't someone think of the children? Suppose X comments, and his comment is endorsed, and goes live. Y sees it, and comments on X's comment. Y's comment gets endorsed and goes live.
If X and Y's aforementioned comments have each received an endorsement from a third party, count that as an endorsement of the conversation between X and Y, and allow their future comments to go live without endorsement if they are children of the X/Y conversation.
Take a look at the several long back and forth exchanges between tptacek and cperciva in this discussion: [1]. It would be a shame to impede such things.