This may be completely undocumented (comment freezing behavior)
afuna suggested to me that perhaps a single-comment freeze was not necessary. It turns out that you can (on both LJ and DW) freeze a thread, then go down the thread and unfreeze lower portions of the thread. It's awkward and you may have to refresh in order to see the right controls, but it can be done, so it's a viable moderation tool.
So yes, if there's one comment that's turning into a problem, but the threads below it have become productive, you don't have to choose anymore: you can just freeze the thread from the problem point, then refresh and go thaw out the productive discussions.