I find the timing weird for Justin to have been (whether he did it personally or had help) behind it. Harry is in the orphanage for four years between his father's death and Justin's adoption. It feels off to me that Justin would kill Malcolm and then chill out for four years until Harry develops his talent. That isn't to say that Justin wasn't watching, though. If it was a year—maybe two—I might be able to see it. But four years is a long time to wait after committing murder.
The one person we know had contact with Harry while he was in the orphanage was Lea. And I could see Lea offing Malcolm, possibly (or maybe even probably) as part of her bargain with Margaret (the agreement WOJ claims would drive Harry to immediately attempt to kill her should he ever learn the full details). And Malcolm might have smiled when he died if he knew it was for a good reason—particularly if it was Margaret's reason.
Pretty sure Lara or Papa Raith offed Murphy's dad, though.