How about grouping stories covering the same current event/topic and ranking them by an aggregate score? This would keep the front page clean while also giving the event/topic a more appropriate rank (i.e. one higher listing rather than 2 or 3 separate lower ones).
6. SOPA making a comeback
217 points | guardian.com 46 comments | eff.org 27 comments | motherboard.vice.com 13 comments
or perhaps:
6. SOPA making a comeback
217 points 76 comments
SOPA Lives on for the International Anti-Counterfeiting Coalition (www.eff.org)
113 points by DiabloD3 2 hours ago | flag | 41 comments
Google, Facebook, Twitter and Yahoo Claim MPAA Is Trying to Resurrect SOPA (www.theguardian.com)
89 points by runesoerensen 3 hours ago | flag | 23 comments
An Undead SOPA Is Hiding Inside an Extremely Boring Case About Invisible Braces (motherboard.vice.com)
12 points by lizzard 15 minutes ago | flag | 12 comments
Groupings would be created on-demand by the editors in response to user flags.
Within the group you could list the links in order of their individual scores. The title of the group could come from the highest ranked or could be manually chosen by editors. You could have separate comments pages, but also a group comment page which is just the union of all the comments.
Later you could take this a step further and include historical posts in the list, thus avoiding redundant comment streams (but only use new votes and new comments for ranking the group -- it has to freshly earn any reappearance on the front page).