look i think it's safe to answer that the m.i.b killed all the remaining passengers of the ajira flight. the other options are chiarles widmore. when we examine him and what he stood for with jacob, he really wasnt the man that ben said he was, so he would most certainly wouldnt have ordered the shootings, and he denied it so i think the writers dont want us to over analyze the situation. the other one was the sickness. well the time elapsed wasnt that long, and since the sickness seems to be related to the monster somehow, that backs him up, and also there would have been at least one survivor if they all fought, but there were no marks, which backs up smokey.