I think the ideal way to reorder would be to consider a comment's post time to be that of its most recent child. This means that when someone replies to a thread, the entire thread will now be the first on the page, with each sublevel ordered in the same manner. Of course, I knew reply to the submission itself would show up at the very top.
This functionality could be extended to the threads page (which relates to a suggestion I made a little while ago) and even to the Startup News page itself, so that we could see which submission has been commented on most recently (because as a parent, its child would have the most recent reply).