If the Choice was meant to make them go NPC, then they would be specifically noted (like the Red Court Infected on page 80).
Keep in mind that most of the fey we see Harry dealing with are those in the upper reaches of power: Mab, Maeve, Leanansidhe. That's some serious refresh cost there. And one changeling we saw go fey became the Summer Lady. There's a lot more leeway at the lower levels - when Morgan is ready to kill Harry in Storm Front for breaking the Fourth Law, the argument is meaningless if Toot doesn't have free will (or something like it).
Last, in the game, the idea of "free will" is a sliding scale. A White Court Virgin in a "Feet in the Water" game who kills using her Emotional Vampire abilities becomes an NPC and loses all of her free will - but the exact same character in a "Chest Deep" game is a viable PC.
I fully agree with just about everything said in this post. One thing though, Mab obviously has free will. Lea has free will or she wouldn't have turned against her nature (as a servant of the Winter Court) to plot against Mab. Sure, she isn't a viable PC, but she sure as hell has some elements of free will.
Toot and other unaligned fey obviously have free will, or they wouldn't be able to pick and choose sides. Simply being completely something other than human does not immediately make the character an NPC, just like being human doesn't make them a PC. Mouse is suggested as a potential character for cripes sake and we know he isn't human, or even apparently an actual dog for that matter.
As far as the White Court Virgin who becomes full Vamp and goes below the minimum refresh level would be interesting to see later in the game. Maybe after a certain amount of time and added refresh, the character could be reintroduced, having learned to control her Hunger. Hmmm...
Also, I might be a little biased about the idea of Fey being playable because one of my character concepts is a pixie.