How did Ebeneezer know anything about Malcolm, like the nature of his "soul?"
Eb soul gazed him, he says as much back in Blood Rites, "as good a soul as I've ever seen."
When Jim tells you, you'll know for certain, assuming he doesn't change his mind and retcon it in some fashion. What you can get from the text is that Eb had orders to kill her and that nobody that Jim has yet introduced was with Maggie when she died. She was alone. Malcolm had to be the one to tell him assuming that Malcolm knew how to reach him. Otherwise it was Morgan.
Unless she was going to have her baby at home, I always assumed that Margaret had Harry in the hospital. I'm not sure whether or not Malcolm was with her when she died. I seem to remember it both ways, one that he was, yet another that he was on the road when it happened. I think, first child and all that Malcolm was with her. When he found out, Eb understood immediately what the cause of death was and who was behind it. Malcolm warned took off with Baby Harry as soon as they'd allow him out of the hospital.