Would they all join the Alliance or Horde? Or will they split up and join whatever faction they want to join?

Basing it off the races they'd probably associate with:

Twilight: Blood Elves (arcane stuff) [Horde]
Rarity: Blood Elves (duh) [Horde]
Fluttershy: Night Elves/Tauren (druid stuff) [Cenarion Circle/neutral]
Rainbow Dash: Dwarves (drinking and adventuring) [Alliance]
Applejack: Dwarves [Alliance]
Pinkie Pie: Goblins/Gnomes [either]

4368521

I agree here for the most part, but with one/two exceptions

Applejack: Dwarves/Pandaren [alliance/either]
Rainbow Dash Pandaren (and likely Houjin at that, considering how often she leaps before she looks)[horde/either]

However, I have a feeling most of them would actually join up with factions like the argents, earthern ring, cenarian circle even if they "join" one of the main 2 if only to help knock some sense into them.

4368227 I don't think they'd join the Alliance/Horde. Probably a more neutral faction like the Naaru or the Argents. Maybe the Cenarion for Flutters.

4368521
You forgot about the worgen. They have druids too. Which is what I have my Fluttershy character on the Galakrond realm as right now. A worgen guardian druid.

4371241

That's true, but I feel like druidism as a whole is more focused on Night Elves (Elune/Cenarius/Ysera) and Tauren (the Earthmother), with a possibility for Trolls (the Loa). They retconned Worgens so much that I don't even bother with their lore anymore.

Either way, I think she'd end up with the Druids, regardless of what race. The main point was that she'd likely be more focused on staying neutral with the Cenarion Circle than siding with the Alliance or Horde.

4371715
Yeah... though if I had to change her class spec. Should it be changed to Restoration?

Well, thinking about the pandaren that joined the horde or alliance based on their philosophies, I think, aj pinkie and rd would join the horde, action over inaction, and twilight and rairty would join the alliance, being prone to thinking a situation over rather the just jumping in. Fluttershy would probably do alli too, if only because she is more cautious, which is a tushui trait, rather then huojin one. Just my thoughts.

I have to agree with 4474182 Pinkie and Rainbow Dash would join the Horde while Twilight joins the Kirin Tor. Rarity would probably be neutral.

4368970 I can totally see Fluttershy joining Cenarion Circle.