I have a few questions:
If what was contained within the box was so dangerous to the balance, why did the Kinkou not destroy every trace of it within the 200 years that they possessed it? Is it because there is some sort of "entity" inside that would escape and wreak havoc if the box was destroyed? Is the box even able to be destroyed in the first place? If someone must take on the knowledge of the box in order to destroy it, why not specifically train a member of the Kinkou to take on its knowledge with the ability to combat its "corrupting" nature so the order may use this power for their own ends?
And on the Kinkou's inaction when it came to Zed himself--if this knowledge was such a threat to the balance, why did the Kinkou not kill Zed for acquiring it or assassinate him during the many years of his banishment? He still had a ways to grow at the beginning of this period by what his bio says. Especially with the fact that he was gaining a following and spreading this forbidden knowledge to others during his banishment... It seems like a gross oversight on the part of the Kinkou. Was Shen's father keeping it a secret? Would the Kinkou really not find out even if he did? It just seems that, as an organization that promotes absolute balance, you would have to really police your leadership in order to ensure that even the slightest bit of corruption or weakness was not allowed to slip in. Because if you get corruption or weakness at the top, it's going to spread pretty fast and undermine your organization's goals.
And as for the action of banishment itself... Was Shen's father the previous Eye of Twilight? The Eye is supposed to remain completely emotionless in order to make decisions based solely on cold logic. If Shen's father was the previous Eye and one of his students acquired knowledge that he believed would ultimately be a threat to the balance, shouldn't he have had Zed executed on the spot once he found out rather than showing him mercy by letting him live? And if banishment was the wrong thing to do, wouldn't that mean it was a spur-of-the-moment emotion-based decision? As in, Shen's father was angry with Zed but attached to him enough to banish him rather than kill him? Had the Kinkou really become so careless that they didn't notice that their Eye of Twilight was losing his logical edge? (Providing that he was, in fact, the Eye. We haven't been told exactly who Shen "inherited" the title from, after all. But just in case...)
Okay, I guess that counts as many questions, actually... I was trying to make sure I was thorough.