This could be implemented minimally and cleanly by having a "save" link appear once you click into the comments for that story, much like how "flag" appears for individual comments. Upvote would +1 the submission and not save it. Clicking "save" would save the submission and not +1 it.
This would let users indicate "This was a very worthwhile story for HN, but I have no desire to read it again" (upvote) or "I'd like to read this later, but I'm not sure it's HN worthy" (save)... or save and upvote. The placement of the "save" link only once you click through to the comments keeps the home page as it was and only introduces one discreet new option.
I hope that's a tune you can dance to. :)