Organization XIII had a good reason for the things they did. However, Sora was also justified in killing them, since they did do some catastrophic things as well as stuff that pissed off Sora.

Xemnas wanted absorb the power of Kingdom Hearts.
Xigbar turned an ancient dragon into the Heartless, Storm Rider.
Xaldin tried to turn Beast into a Nobody.
Saix kidnapped Kairi (big mistake).
Demyx caused some havoc in the Underworld.
Luxord awakened the zombies in Port Royal.
Marluxia tried to manipulate Sora.
Larxene did basically the same as Marluxia.

All of those things that they did, while you could say they were justified, that doesn't necessarily mean that OXIII is completely faultless. Technically, you could something like a thief stealing money for his family is justified, but that doesn't make it acceptable.

As for the others...

Axel became his ally, Roxas essentially IS him, and Sora never even met Lexaeus or Zexion.
The only one who probably didn't deserve to die was Vexen, since he tried to help Sora in Castle Oblivion. But then again, it wasn't technically Sora who killed him.