[PureHarvest]

You have to consider the context.
Flame weeding is to control recently germinated seedlings after you have tarped or tilled the soil. Not to say a flame won’t kill mature plants, but that’s not the point of the technology.
As far as killing microbes, etc, you are not putting a dent in the population when you use the flame weeder as mentioned above. You are singeing seedlings, not fire bombing the soil.
The collateral damage from proper flame weeding is neglible compared to tillage which burns up organic matter quickly, and destroys soil aggregation and structure.
Organic corn growers are moving to flame to elimate all the soil disturbing cultivation steps they take for weed control. They are not burning down large weeds to prepare a seedbed, rather hitting young, newly germinated weeds.
Bottom line, proper flame weeding is a fast pass with the flame that cooks recently germinated weeds on what were very recently bare areas. Only a small fraction of the top inch of the soil is affected by the heat and does not ruin your soil fauna.