Consider whether we might be better off without that feature, which also makes it super easy to keep aging threads alive, which is something HN has subtly discouraged thus far.
I've definitely been considering it, but it's also the most-requested feature by the people who've been using the highlighting so far. I think as long as we make it relatively passive, i.e. you still have to scroll to see the new things, it might not be too much of an unwanted catalyst.
Worst case, if it did turn out to have a major negative effect, I hope (I pray?) we would have enough killer instinct to claw it back.