It's easy to design a system that prevents the flagging in this particular case, but will it be better overall?
I feel that it's quite inevitable in a community like HN for this theory to get flagged. It's undesirable, but the alternative is worse.
Why? Because at its core, the HN community is a polite, considerate one. We try to apply the charitable interpretation when possible.
The postings about the lab-leak theory could be interpreted in a charitable way too, but unfortunately, the lab-leak theory has a dark undercurrent: "China is bad". Of course, lots of people on HN are smart enough to understand that the lab leak was a joint China-US fiasco (of stupendous proportions). But they also understand that these nuances will be lost in translation. "China bad" is the only thing that comes out.
For more than half a year there were numerous attacks on Asian people in the US. This was not just a theoretical exercise, it resulted in actual hate in the US.
So flagging the lab-leak postings was in line with the HN's tendency to go for the charitable interpretation.