That actually usually depends on the knights in question, funnily enough. The usual thing to do for a knight is simply to mow everyone down, since part of their code is "You must show compassion and all kinds of things to every, except your enemies". However!
There are officers and knights, like Caedmon, whom, if the knights surrender, will take prisoners. I can't speak for anyone else, but basically, Caedmon will never injure a civillian. He would rather capture them. If a Mechanist/Declarum soldier fights him, Caedmon sees this as the other 'mon having known what he was getting into and accepted his fate and basically fight him to the death if need be, but should he surrender before even fighting, or during the fight, he would try to take him/her prisoner.
Again, can't speak for anyone else, and I'm fairly sure the council would only ever want prisoners for interrogation and nothing else, but you can be sure there will be knights who would want to capture Mechanists, rather than kill them.
Long explanation, sorry about that XD