One reason Miko snapped

[Imgran]

Nah, he didn't have to bend over backwards, he just had to turn Belkar loose.

Belkar is the sadistic little X factor here. Roy's willingness to associate with a clearly and unrepentantly evil character is what convinced Miko of his guilt-by-association. It was the run-in with Belkar during the trial, his murder of multiple Azure City guards, and the Order's subsequent defense of Belkar that turned Miko against the order, and Shojo's collusion with the Order that caused her to snap.

In one way Miko was right. Despite your alignment, shielding an evil character from the consequences of his actions is an evil act. What she didn't get was that the only possible consequence of an evil action is not a death at the end of her own personal katana. The order had no problem exposing Belkar to the consequences of Azure City law. They just weren't going to stand around while he was summarily executed without a trial.

Miko was an extremist, and extremists don't believe in tones of gray or half measures. Once you accept that and combine it with Belkar's little caper during the trial in which he demonstrated his own clearly evil nature, and the sheer level of stress Miko was under to begin with, everything else clicks into place like it was meant to. And one complete lack of either space, time or willingness to examine the premise later, you have half a fallen paladin dying in the ruins of her former master's castle.