Well, I have an idea for rewriting the flavor text of the Shiba protector. However, I'm not sure how well my idea would fit in with your world either.
Essentially, the class's abilities fall into 3 areas: combat abilities based on inner focus, defenses against magic (SR, bonuses versus spells and spell like powers), and ways to assist friendly spellcasters. The class is excellent for monks, so there's probably a lawful focus. The feats required are defensive in nature.
The way I see things, a typical society in a DnD world is going to be under a lot of pressure. First of all, there's the same stuff that happens here. Competition, war, armies, plague, famine. While magic can reduce some of the problems here, it can't completely negate them. Even if there are lots of clerics able to cast Cure Disease, if they don't catch an outbreak right away, it can spread beyond their ability to cure. Second, monsters provide a significant external threat. Finally, powerful individuals can, be themselves, be dangerous from within or from outside society.
I see the Order of the Phoenix as defenders of order and benevolence. Order is needed lest civilization be swept away, and benevolence is needed lest order forget its purpose and stop protecting and helping people. The group is made up mostly of skilled and competent people that aren't evil or chaotic. Skilled warriors and spellcasters can help deal with external threats like monsters. Because of their organization, they can exert some influence on rulers and other prominent groups to strengthen order. And, because it consists of intrinsicly skilled individuals - especially monks and spellcasters - strong rulers attempting to supress the group will run into some difficulties. It's not like you can confiscate a monk's weapons, so he'd always be a relatively inconspicious threat.
The prestige class represent special training availible to members of the order with advanced skills, and who have proven themselves worthy. Because normal people have little defense against magical attacks, spellcasting characters and creatures are great threats. Therefore, the training increases one's resistance to magical attacks. Similarly, some threats are best dealt with magically, so one can learn to assist allied spellcasters. Finally, the same inner focus and will that strengthens the mind of the initiate can be refined into an incredible combat talent: with great will, one can surpass his or her normal limits.
EDIT:
I think my character is ready too.
