Morgan dies in "Proven Guilty", after finally understanding that while not being able to uphold the White Council's law as optimally as possible, Harry's the best guy the Council has to stand up against the ever-encroaching Red Court. Long story short, Bianca got roasted by Dresden and Ebenezar dropped a Soviet satellite onto Duke Paolo Ortega - Bianca's hubby and Duke of the Red Court.
As to why McCoy did that; it's revealed that he has direct connections with Justin DuMorne and that he essentially was the White Council's one-man Black Ops team. As the Blackstaff, he had authorization to carry out deniable ops of an arcane nature - including busting a Duke of the Red Court if that could alleviate the war effort in any way. This is going to bug Harry, seeing as this "license to kill" approach means that Ebenezar did indeed have and certainly did use his right to carry out black magic for the White Council's sake. He literally is the only wizard in the book who has the legal right to do whatever the fuck he needs or wants.
This also explains how he managed to save Harry's life. He invoked his position as Blackstaff to get the Council to commute Harry's death sentence, as a kid, and turn it into the Doom of Damocles. He also invoked his position to more or less pick up tutoring duties after DuMorne's death.
In the later novels, the bat-vamps are after wizards something severe, forcing said wizards to negotiate with the Sidhe Queens for the right of passage through the Nevernever.
As for the Merlin, well, Arthur Langtry's really just your standard politician. He can't acknowledge that things are going horribly wrong for both the world's population of practitioners or the unsuspecting mortals. Not because he doesn't want to, but because allowing people - especially powerful people with the ability to mess with the forces of Creation - to flip tables in sheer panic is absolutely not a good idea.
Add to that the normies and their armies and thermonuclear capacities and, well... You start to get an idea as to why the Merlin has to pretend like nothing's happening. Denial is keeping everyone safe and sound, tucked away in their personal routines, while the Wardens are out there bleeding and dying to keep the Red Court at bay.
By the time you get to "Ghost Story", the latest novel, things have utterly and completely gone to shit. The stage is now set for what's been referred to as the final apocalyptic trilogy, beginning with "Hell's Bells".