True. After all, Pigma may be a character everyone hates. But he is integral to the story and even though he at times like to remind Fox that he was responsible for James McCloud ' s death, wouldn't it be Peppy's choice to shoot him down as a personal score? This actually reminds me in the 2011 Thundercats series where Grune betrayed Panthro, Lion-O, and his father Claudus(which Grune was responsible for Claudus's death).
Anyway for Krystal now, at least this puts her in a better position for DLC candidate to be playable after the whole King K. Rool Mii fighter costume fiasco(feel bad and sorry for the DK fans on this). So I have a feeling that she still has a great chance to be in the game. Even if she doesn't show up in Zero, I'm sure she'll be in future entries in the Starfox series. She's a popular character from the series after all not to mention the huge amount of support she has been getting in the Miiverse as well.
Regarding about Zero, since the game is basically a reimagining, I'll bet Nintendo will pull off a Zelda here and that the Starfox series has several timelines. What do you guys think? Anyway, I'm sure we'll hear more on Starfox Zero anytime soon.