Ah, it could be difficult to merge two comment threads when one of them is ordered chronologically and the other by karma. Let me think...
I think that in the chronologically ordered threads (the threads written before the comment ordering was implemented), all old comments are actually top-level comments, and whatever is below them was written much later, right?
In that case, it might make sense to make a mixed ordering, which would order top-level comments chronologically, but everything inside them by karma. Make this default for the ancient articles.
Then a possible way to import the SEQ RERUN comments would be to create a top-level comment saying e.g. "SEQ RERUN 2012" (the year, in case there were multiple reruns of the same article), maybe make it the first comment by giving it a fake date (maybe year minus 2012), and moving the comments from the rerun under this comment.
Another possible approach would be to do this the other way round. Create a special comment flag that says "the comments directly under this comment are sorted chronologically no matter what". In the ancient articles create a top-level comment saying "ORIGINAL COMMENTS" and move the original comments under this comment. Then move comments from the reruns directly under the article. (Or maybe under "SEQ RERUN 2012". And disallow creating manually new top-level comments.) The reason for this second approach is that there probably fewer original comments that rerun comments, because the community has grown in size, so it makes sense to treat the original comments as a special case rather than the other way round.
(I am just randomly thinking out loud. I am not an admin, and not going to implement any of this. Maybe this is not even a high priority.)
I'm re-reading sequences now and I'm noticing eye-opening things like so many have SEQ RERUN, useless copies that clutter up the link space while having very few comments that they seem to be intended for. Can the moderators do something about this? Remove links to them, maybe even delete them by moving the comments to the original posts. (I don't know if there is functionality to do this, and also how morally acceptable it would be, and if anyone but me is worried about these problems, maybe no one else needs to "fix" this?) And also I notice, that in the old entries, the answers are not child comments, which creates a terrible confusion when reading by karma, when it is not clear what the question was and where to find it. (Same requests and questions here)