Comment by Natsu

What about this for a sketch of an idea:

Give us the ability to cite 'other sources' for the same story (ideally it should be smart enough to dereference other HN submissions if that's passed in). Then mods can, if they so desire, merge comments from separate discussions into one pool.

Finally, for the alternate links, you could consider allowing users to vote the best source. I say 'consider' because I'm a bit iffy as to how it might work out. I don't remember any significant controversy over which story was best and mod rule might be for the best. There are also issues with how you score a poll when some options may not have existed during any given vote and HN tends to use approval voting in polls.