How about the murder of Sahra Covenry, the slaughter in Fal Dara, Temaile's ideas of fun, the torture and murder of that Kinswoman in LoC and innumerable other acts? Or did you forget that the incident you cite was ALSO the work of a Darkfriend! You DO remember that Jaichim Carridin was the commander of that project, and Bornhald's final command to Byar is to report on the actions of the Questioners to Pedron Niall. Plainly, he does NOT think this is usual, or has faith that such behavior will not be tolerated by the Lord Captain Commander. There is no indication that 'Bors' was acting normally either, since Niall reprimands him for screwing up his normal mission. Bors was acting under Ba'alzamon's orders in that operation and for the external impression of his actions was threatened with being turned over to his own Questioners.

Bornhald is disgusted at the excesses of a commander secretly working for the Shadow, and like all the other NORMAL Children, resents the Questioners and notes how they act apart from the others and are not like real Children of the Light at all. They are one of those politically necessary encumbrances that groups which wield power for good or ill must endure, despite their disagreement with them. You claim they don't investigate properly, but we see no evidence of how they investigate one way or another, only the claims of their enemies and the sullen resentment of people they chastise for their shortcomings (who, despite your claims, are generally alive to piss and moan). We have seen no cases of the Children hanging the innocent in a book, and the one authorized execution (as opposed to atrocities in the field by Darkfriends) is of people we know to have been guilty all along.
Anyway, give me a man who stirs up passions against the Shadow and inadvertently motivates some illiterate peasant to go too far and sweep out an undesirable scumbag who happens to be innocent of Darkfriending, if nothing else, than the woman who terrorizes and traumatizes a loyal servant for merely inquiring about the existence of the Black Ajah and thus allows the most dangerous Darkfriend group in the world to thrive unchallenged. The Tower's approach and the Children's are simply opposite extremes, and equally justifiable and equally flawed.