I had a background generated that I was pretty sure was going to have Pallegina be a Kind Wayfarer (I had her disobey her masters), but instead when I got her she was still the Canc Suloias subclass.

 

FYI, It turns out that Wrath of the 5 Suns is pretty garbage, it does about half the damage of flames of devotion for twice the Zeal cost, and cannot be upgraded with Sworn Rival to refund any of the cost upon kill.

Have Pallegina disobey her orders WITHOUT giving Galawain the souls.

Source: https://pillarsofeternity.gamepedia.com/Pillars_of_Eternity_endings

 

That's assuming she isn't bugged like Eder (Eder ends up being a nonsensical mix of all his endings no matter what state you import him from or set him to)

Even if she 'joined' the Kind Wayfarers (like in my ending, she even mentions doing the caravan work), she still has the Five Suns. From what I've heard, she can't actually game mechanically be a Kind Wayfarer.

If you get her un-fired and she joins you, it is for the ducs and she changes back from the wayfarers to the five suns for your party.

It makes sense.  Paladins are powered by the core beliefs in their souls, and even if Pallegina was kicked out of the Five Suns military order, she is still, at heart, a patriot of the Republics far more then she's a Kind Wayfarer.  The Republics abandoned her, not the other way around.

Damn this game is an entangled mess of bugs. I really don't think releasing a game in this state is acceptable by any measure, and I cannot honestly recommend the game to anyone without even knowing how much of this game is bad writing/scripting and how much of it is simply bugged dialogue/flags.