He showed that he is willing to use balefire on a large scale to destroy a whole palace with a Forsaken in it, even if he kills innocent people alongside the Forsaken (and even if all those people were "drones", they are still innocent and not the real targets).

As it's shown later in TGS, Rand starts then to see balefire as a common weapon. He already contemplates to balefire Tam and all the Seanchan. The next possible step would be that Rand considers to balefire whole cities, which don't bow to him or if he just believes that a Forsaken is inside the city. Ultimately such an attitude threatens humankind and the Pattern. Therefore balefire is forbidden and to use it widespread as Rand did an atrocity. Even the Forsaken don't want to use balefire this way anymore.

Besides that, Min and Nynaeve apparently - wrongly - believe that someone who was balefired can never be reborn, which would make its use even more horrific.