Well, regardless of what RJ may or may not have implied in later Q&As about balefire, I re-read that scene a few times and Min and Nynaeve were horrified because in their understanding, he burned innocent threads from the Pattern never to be Reborn.

Without having omniscient abilities, neither would have known that killing one villain was worth sacrificing hundreds of innocent lives in a permanent matter.

I think this is one of the scenes that really made Nynaeve come to the realization that Egwene, Elayne, Moiraine, Cadsuane and the Wise Ones had already come to; if Rand adopted such tactics, saving the Wheel using such scorched earth practices, he would have crossed a line where what he saved might not be any better than what Ishamael or any of the Forsaken intended.