Alright this is my take on this issue
1st I love the setting as is. I love the factions and I love the whole cold war theme. Shadow factions using a neutral organisation to further their goals is a very cool twist on the dungeon crawling theme.
2nd I understand the problems with Evil characters but I think that within the setting as it is presented the factions definitely include evil people. It could be the Andoran rebel who has no qualms about killing an entire family of nobles to prevent succession, the Quadiran capitalist who values money more than lives, or the Osirian archeologist obsessed with finding ultimate power but some of these people will definitely find themselves in the pathfinders. But we have to remember the rules of the pathfinders which include cooperation. Pathfinders are people who are used to dealing with people with different cultures and different values and even if they don't agree with them they can work with them.
3rd The metagame problem comes with the paladins who cant be with a group that includes an evil character...well paladins are exactly the type of people who find the idea of a shadow war distastefull. They would rather be on the front lines fighting it out than in the shadows making deals with the enemy for use later.
My suggestion for a solution is to go easy on allignement issues at least for year 0 or Chelaxian faction members are going to constantly have to justify their actions.