My theory has it that he knows a future and it could be 'best' served if Harry got out of Murphy's way. He'd use his knowledge of some future to bind his father to prevent him from doing something 'stupid,' something like what choice he made in GP.
The alternative could be that he is Mab/Murphy's son but not Harry's. In this case he would still want Harry out of 'Murphy's' way as he believes she more capable than Harry to deal with some things. If the relation is true, it could also mean that Murphy has an intrinsic "I can't die" property as she has to TT into the past to assume the mantle to 'spawn' Marcone. This fact, that Marcone is Mab's son, would put people in the know of his heritage on guard against him but wanting to use him against Mab. This is why he has been repeatedly the subject of so many plots. If he is Harry's son, then it seems reasonable to assume that Harry has a "I can't die" property until his conception is brought about. This tidbit though really significantly puts holes into the idea that Harry sires Marcone as we know -Harry summons Harry's to kill. It is still an area under development, but there is denying that there is strong interaction between the choices and actions of Harry and those of Marcone.
In the case of no familial relationships, I still think he has via deals etc some clues as to what problems spots on the horizon that needs to be headed off. He will use Harry judiciously etc sometimes when he needs Harry to do a job, other times sending him away when he needs that to happen too.
