I agree with wedrifid, and would prefer that this doesn’t happen.
One problem is comments are “non-local”, as long as they are above the bad-comment threshold, they appear in the recent comments. Allowing people to have stupid discussions freely will pollute the recent comments section (and this was actually one of the reasons for the recent implementation of the karma threshold).
If LW supported marking some threads as “comments don’t appear in recent comments”, then it wouldn’t be such a problem, although there is also the risk that the low-quality will start overflowing into the rest of LW (maybe?).
There are a few other “crackpot indices” around. John Baez has a famous one, and Scott Aaronson has one in that vein (mostly specific to mathematics papers though).