This is so horrible... I like it.
I thought the ending was like a repentance for D.Va. Since it was mentioned that the Meka was only half as well as her body, I thought that she had herself fused to the machine, to prove to Mercy that she was sorry about her pride. It was this realization that crushed Mercy into despair. Seeing that D.Va sacrificed herself, her body and her ideals, just to meet her in the battlefield and save her. Or maybe it was just a really powerful attack that ripped her and her Meka in half, I don't know.
The message could be more general, such as the atrocities of war bringing out the worst in everything. The doctor herself causing the injuries as well as a young pro gamer being enlisted for war. That moment where Mercy was desperately trying to revive D.Va, scrambling around knowing she was the cause of it all and the realization that it was already too late... For the doctor, that was beautifully heartwrenching.