Main takeaways:
1. Donald Morgan and Maggie Le Fay knew each other - and had an association strong enough that Morgan would protect Harry.
2. Morgan was actually protecting and testing Harry for most of his life! Margaret made him promise, which means towards the end, whatever their previous relationship he trusted her enough to make that promise. And all his bullying of Harry was to ensure he wasn't the monster that clearly some thought he had the potential to be. More on that below.
3. Malcolm's death: this is the second or third hint that it was unnatural. My money is on DuMorne as he obviously had been building a plan for some time to get his enforcers, and I am sure he would have been well prepared to kill Malcolm to get Harry. And it wouldn't surprise me if he used mundane methods like Ricin poisoning in order to simulate natural causes. Although the possibility remains he did it with magic and covered it up...I can't remember where but I am reasonably certain Justin was an able mind-mage.
Also - the fact that Harry disappeared from everyone whilst under DuMorne is further evidence of a conspiracy. Magically, physically and bureaucratically covered up is just too clean, and I am sure Justin had help. Perhaps from Peabody, perhaps also from others (both in the Council and otherwise).
4. Morgan thought DuMorne was a bastard. Probably for what he did to Harry, but perhaps in the same vein as Cristos. They would have been colleagues as Wardens so one imagines DuMorne was pretty nasty, if Morgan (who could be quite the bastard also) thought he was. That says something right there.
5. I will break down this sentence as there is a bit to unpack.
From then on, we could not be sure that the child was not molded to be a creature of Nemesis.
Morgan knows about Nemesis. This isn't totally surprising as he was a top-level warden, and with power comes knowledge and Morgan was pretty powerful.
He doesn't actually theorize Harry to be infected - I suspect he wouldn't have even gone to him if he did, which says something else to me.
I think he IS implying Justin was infected. That would make sense with why Justin became what he was - however it is just a theory. Justin could ALSO have been merely working for some other Nemesis-infected person.
The "we". He almost is certainly NOT referring to the White Council as a whole, and probably not even the Wardens. My guess is that he is referring to a certain group
within the White Council, somewhat like the Grey Council, but perhaps a taskforce led by or commissioned by the Senior Council (likely the Merlin but quite possibly the Gatekeeper). I am sure Anastasia was part of this group too. Think secret police.
5. Confirmation of the fact Justin might not be dead - Morgan suspects that it could have been simulated. Now we know Harry believes he murdered Justin, but if it was a ruse, he might have been fooled and perhaps even agents on the Council might have helped cover it up.
6. Morgan seems equally disturbed by the fact Harry might have killed Justin outright at sixteen - probably because as I have speculated before, Justin was no slouch. If Harry beat him then Harry might just as easily be the monster they suspect. Think monster in the sense of Bonnie, a being "born of the spirit of a fallen freaking angel and the mind of one of the most potent wizards on the White Council. She's going to born with knowledge, and with power, and be absolutely innocent of what to do with them.
a lot of people would call that monstrous" - Skin Game, ch23, p170. Harry might have freakish, monstrous power potential. Curiously also in that book, Grey tells Harry that he didn't choose the legacy she left him
with her blood and she was a (according to Grey) a piece of work. One wonders exactly what blood magic is performed in making a starborn, and what was in her blood that made it possible. He might have been referring to simply being her child, and/or being related to Eb as well but I think it is more to do with the Starborn stuff.
7. Harry's potential for destruction is clear - Morgan thinks he should have been killed as the risk was too high. The fact he refers to him a Destroyer seems pretty clear, but I will get into that later.
8. Interesting that Morgan knew of the family connection between Harry, Margaret and Ebenezar. Well in the circle of confidence.
9. Morgan says he is testing him to draw out any controls that may have been emplaced. I believe he is referring to two things: Ancient Mai's argument for not keeping Harry a wizard in Summer Knight, that the Gatekeeper explained. Ancient Mai believed that DuMorne's teachings might have shaped in ways that he can not see. I believe that was a bit of layered double-speak. They were clearly about the lessons both direct and otherwise that Harry learned from his time with Justin. But I also believe she was worried about Nemesis, either infecting or manipulating him through others. And general black magic taint - which Morgan also refers to in the same paragraph of his journal entry.
The second thing he might have been referring to is enthrallment, very fine enthrallment. I would say the fact despite everything Morgan threw at him Harry didn't turn out to be a sleeper agent is probably a good indication he isn't enthralled, however it isn't concrete. Perhaps Justin was just that good that it is buried so deep that it will only show up right at the end.
10. Morgan implies that black magic taint can be concealed.
11. Morgan, despite everything, still goes to Harry despite not knowing if Harry is a terrible monster time-bomb. Which both shows how desperate he is but also how seriously people are worried about Harry - more than a mere warlock.
12. The enemy has invaded the Senior Council by Turn Coat, according to Morgan. This is before Cristos is appointed. He could be saying that Nemesis has infected one of the Senior Council...my guess would be Mai or Merlin but anyone could be. But Morgan could also be saying that the machinations of Nemesis have managed to get between the Senior Council.
13. Quite interestingly, he talks about the web of conflicts between either the Senior Council and the Enemy, or the Senior Council itself. I think much of this will be revealed in Peace Talks.
14. I think this whole passage released before Peace Talks is to set us up for it. I think Nemesis and maybe even Harry's birthright will become more prominent in the next book.
15. Morgan had his doubts and by the end realised he was wrong about Harry. Harry might be Hellboy, but if he's on the side of the good guys I think things will work out. Seems like he is the kind of weapon that can work out really well, but also blow up in your face.
16. Is Elaine a Destroyer too? If so, the fact that she is flying under the radar is pretty worrying.
17. Pretty sure the reason Morgan was sure there was no "Black Council" is because of Nemesis. He understood that was a simplistic view of a far bigger problem. Which isn't to say the Circle isn't an organization, but they are probably more than just dark wizards with an axe to grind and probably have many other supernatural entities on their roster. And maybe they are nemfected, or just some, or maybe not. But almost certainly they are linked to the Outsiders...
18. What the hell is a Destroyer? Last we knew Harry was merely referred to as Starborn or Child born of the Stars. The only thing we knew about them is that they were born with the potential to wield great power of the Outsiders. Doesn't smack of destruction directly. But what if Harry is more than merely a potential leader of Outsiders, or gate opener etc. What if he actually can cause mass magical destruction on his own? Would be very Dresden. And could explain why so many people want him on their team, or dead.