The Organization is not evil, nor good. It is neutral.
Yet there are members that are corrupt and are evil.
This means that the Organization is not some sort of Malificent wannabe that wants to control the heartless, but in my eyes and organization that wants to restore the balance of light and dark.
But some of the members want the darkness, and they are trying to destroy the keyblade weilder, the person that can restore the balance...
Mickey is one of the good/neutral Organization members if you ask me. Riku is definetly neutral/near dark... which is not his fault, he is trapped in his confusion...
And you have the BHK... But he starts to believe that the Organization is definetly evil, and DiZ wants him to destroy the Organization. BHK, who believes they are evil will do his best, while in fact the Organization has one goal: restore the balance of light and dark...
Don't you think so?