Its actually quite simple - push the thread with the latest comments to the top. But in order to stop such threads from hogging the front page, there can be another tab for 'active' threads that people can visit to check out latest discussions. The current front page remains unchanged, with whatever algorithm that's used to order the threads.

This is a good idea, and I'd be very interested to see if they ever added that, as it would essentially solve the long running conversation problem that exists on HN now.