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Well seems like Johnson wants to raise the boy as his own son, all we need now IF possible, Seleene to pop up behind him, or face glomp him, like a little family lol. Or the eldar ghost girl becomes corporeal, but has a figure of Seleene (we can wish right?)
So, it seems Malal's tactic here is finding that little speck of hope within the ruins and pulling it out for the protags. The generator of the crisis suit, the shard of the avatar, the child. But what was up with exploding Skraat?
Johnson and Malal seem to be referring to just the child's body when speaking of their arrangement (though this is a rather literal reading).
Theoretically, the child might now be an empty shell.
Of course, there are a couple Eldar souls just hanging around...
And maybe a Durchii one as well... (though the odds on that one seem rather long, sadly).