Like you said, this change may lead to the case that "high quality comments on any threads that aren't on the front-page" will not be shown. The lack of those comments and subsequently the lack of a vibrant discussion might discourage other users from participating, leading to the article never making it to the front page.
I foresee this causing an even worse problem than low quality comments: The front page will be flooded with stories that make it their not because of the quality of the accompanied discussion, but because of the "clickability" of the article title.
However, it seems like there is a relatively simple solution. The number of "endorsements" required to activate a comment could be inversely proportional to the articles points. Or as some other users have suggest, it could be inversely proportional to the quantity of other comments on the same article.
I foresee this causing an even worse problem than low quality comments: The front page will be flooded with stories that make it their not because of the quality of the accompanied discussion, but because of the "clickability" of the article title.
However, it seems like there is a relatively simple solution. The number of "endorsements" required to activate a comment could be inversely proportional to the articles points. Or as some other users have suggest, it could be inversely proportional to the quantity of other comments on the same article.