Timing is everything, who arranged for Morgan to be away on a mission when Malcolm died, and young Harry dropped off the radar screen? Morgan says he arrived on scene less then ten hours later and Harry had already disappeared. Really? No records anywhere of what happened to six year old Harry? What is weird about that is as a Warden of the White Council, you'd think that Morgan would know some pull to get access to those records. Someone on the Senior Council or even Luccio would have political connections of that kind.
Of course, we don't have the information we need to figure this out, but I will try anyway. Just because Luccio is the Captain of the Wardens; and she probably gave Morgan the orders which sent him away from Harry and his father, that doesn't mean it was her idea. Captain Luccio could have been given a mission to accomplish by a Senior Council member, a mission that required someone with Morgan's knowledge and skill set. That leaves us with an old problem, which Senior Council member of that time was a traitor?
We can probably eliminate Aleron La Fortier because he's dead. Ebenezer wasn't a Senior Council member at that time and I doubt that when Eb was acting as the Blackstaff he would have ever needed to consult with Captain Luccio. Cristos wasn't on the Senior Council then either. If Arthur Langtry, Ancient Mai, LTW or Martha Liberty was and is a traitor, they all sure have had a lot of time to be doing traitorous things without accomplishing very much. So I discount all of them as traitors. That leaves The Gatekeeper and a Senior Council member we've only heard about, Simon Pietrovich.
If it was the Gatekeeper, couldn't he just screw up the defenses at the Outer Gates by letting a bunch of nemefcted individuals get through or misdirect Winter's forces so the Outsiders could break through in a big way? That leaves Simon. I don't think Simon Pietrovich is dead. Unlike Aleron La Fortier, I don't think we heard anything about his body being found. My guess is that Simon is Cowl. It would explain how Cowl knew that the wardens were nervous about Harry. It's one thing to know about Harry. A ton of people and not people have known about Harry, but to know about internal White Council gossip is another thing.
About whoever made Harry seemingly disappear from the face of the earth, Mira you mentioned Lea later in your post and she is the obvious suspect, but just to nail it down a bit better, remember that Jim has told us that Margaret LeFay didn't make the best deal she could have when she bargained with Lea to protect Harry. Margaret probably didn't think to get protection for Malcolm Dresden because he wasn't part of the magical community. Margaret's deal probably didn't preclude Lea from making a separate deal with Justin DuMorne and later making another deal with Harry. Lea would have seen Justin as a good match to teach young Harry how to use his abilities and also calculated that she could live up to her deal with Margaret by eventually helping Harry to defeat Justin. So I think Lea either killed Malcolm Dresden or looked the other way while Justin did. Until Lea was forced to hand over her contract with Harry to Mab, I think she had gotten the better of Margaret, Justin and still had a long-term hold on Harry.
What I want to know is whether Luccio will ever show what Morgan wrote down to Harry. Harry may need the clues in Warden Morgan's journal to figure out who the traitor is. Also, LTW personally investigated Simon's fortress at Archangel. Seeing as River Shoulders told Harry that LTW is near the end of his road, if Injun Joe learned anything interesting investigating the Red Court's attack on Simon's personal HQ, it's about the time he shares that knowledge with someone else, maybe Harry. I'll be very interested in any conversations Harry and LTW have in Battle Ground. Finally, after reading Morgan's final journal entry; assuming she did read it, Captain Luccio should also be putting pieces together and wondering about the unlikely coincidence of having to send Morgan on a mission, when he could have stopped young Harry from being disappeared. However, if it was Simon who gave Luccio her marching orders, and she believes Simon really was killed by the Red Court, then to Luccio coincidence might make sense.