Horde and Alliance NPCs really get similar treatments when it comes to dungeons/raids. You have the ex-faction NPCs like Nazgrim or Fandral who are killed. You have the minor NPCs like Mestrah and Anathos who are killed, and then you have the major NPCs like Gelbin and Jaina who are injured. Even major ex-faction NPCs like Garrosh and Sylvanas aren't killed; they're captured and put on trial. The main difference is that Horde's major NPCs are turned against the faction more often than Alliance's are, while Alliance's major NPCs tend to embrace the Horde more.