Ok, what game were you playing OP?
(1)The Organization has never once aided Sora in killing heartless. They spent the entire series summoning heartless to him so he can kill them and they get the hearts they captured. (2)Second of all, while all of the Org wanted hearts (except Xemnas who wanted to be a god, is this really heard to figure out. Seriously, why do people get his motives mixed up >_>) they com mitted mass genocide, killed many people and worlds to create Kingdom Hearts. If you do insist on defending them, then please tell me what justifies the sacrifice of millions for 13 people?
(3)Yes, Sora is semi ignorant, but he never thinks of himself as invulnerable. Saving the entire universe just gives Sora the cockiness that he has in KH2. Seriously, you go save the whole universe and then NOT believe you aren't a powerful SOB.
And KH isn't the type of game to kill off the good main characters. (4)TAV aren't even dead. Aqua is a pile of armor it seems, Ventus probly has his heart sealed in Sora, and Terra is probly off being Xehanort, or part of him. (5)I honestly think that if a main protagonist DOES die, it'll be Riku. He has so many sins, and Im sure he still has problems with his past. If there is an instance where someone needs to sacrifice themself, it'd be Riku. (6)Or we could just offer Donald, no one likes him anyway.