That's a good question, and I've thought about it a bit over the
intervening three years.
tptacek was shooting from the hip that day, and posting a lot of his
ideas (and regular annoyances), one per post, in rapid succession, but
without the time needed for a lot of planning or analysis.
His idea of "sincere flag" could be improved by combining limits and
disincentives to prevent high-karma accounts from just always setting
the "sincere flag". There could be the usual limit of a karma threshold
for the feature. There could be a limit on how many times or how often
the flag could be used. There could also be a disincentive such as
making each down-vote or flag cost a lot more (10x/100x/1000x), or
making the use of the flag cost something substantial like -X% of all
account karma.
With the right combination of limits and disincentives, his idea might
work, and only be used on special occasions rather than be (ab)used
constantly.