It's reasonable to assume Mattie's first words would have corresponded to what Ruth Hale later says about her: that it's a pity she lived, because if she had died, Ethan might have lived.
Given that Ethan has lived, the statement doesn't make literal sense. But the real meaning is perhaps that if Mattie had absorbed the entire shock of the collision with the elm tree, then Ethan would have been saved from the crippling injury he's undergone. Or, even more probably, it means that with Mattie's death, Ethan, regardless of his injuries, would not have been burdened with Mattie in her disabled condition, as he is for the rest of his life.
Since the plan of Ethan and Mattie was to commit suicide, it would make sense if Mattie, upon first awakening and realizing she's paralyzed, would have said, "Why didn't I die?" Any person seeing herself permanently incapacitated for the first time might say such a thing even if suicide hadn't been her intention.
What Mrs. Hale remarks is that there is little difference between the living Fromes and those in the graveyard. The tragic outcome has been that Ethan, Mattie, and Zeena are stuck together in a situation that is immeasurably bleak. The physical impairment of Mattie and the less severe but very real crippling of Ethan have compounded a dynamic among the three of them that was already dysfunctional before the "accident." It's a love triangle in which there is no possibility of resolution or escape but only endless suffering. This is what Ruth means by describing the three of them as essentially being the living dead.