Considering that a post can hit the front page and then disappear within hours, I don't think that it is necessary to organize by time.
The most relevant comments (calculated by number of upvotes in a given period) are at the top and the spammy ones (or those that don't add anything to the conversation are the bottom).
This would happen simply because the commenter posted outside of the time the topic was most popular (most viewers).
Sometimes I do see golden comments stuck at the bottom because the poster was late to comment. It's bad but there really is no easy fix.
It's up to the community to upvote all quality comments (and submissions)...even if that means having to scroll to the bottom of the post to find great comments.
Like pretty much everything else in life, the system isn't perfect. I'm sure PG would listen if you have a better way of implementing comments.