Victor Sells, once discovered, would be easily taken out by a prepared SWAT team. His little demon too.
The Loup Garou would be the hardest to deal with, but FBI agents would be discovered quickly by other government forces if the Supernatural was known about. In fact, it would be much harder to influence governmental or other agencies in general once they got wise to things. As for the Loup, if you can't contain it (that would probably need some help to do easily), then they could reluctantly kill him in human form. Though who knows if Physical Immunity works against tanks and missiles?
Ghosts would also be hard to deal with, if we go into the 3rd book. Almost need to have magic users to help with that, I think, unless there are conventional stuff to assist. Vampire abodes wouldn't be tolerated though, and the Vampires quickly killed, so the Bianca angle just wouldn't exist. The Reds might seem potent, but if humans knew they were around they'd be forced into hiding and get wiped out, wherever they hid. Flesh Masks and the capacity for infiltration would be something governments would allow to persist once their inherent evil was understood (there might be some hijinks at first). Going to Changes for a moment, that whole ritual would get stopped pretty quick by shooting missiles and the like there, or at worst, a nuke.
As for Summer Knight, that's a bit trickier, but I guess if things got really out of whack and went hard Winter, we could just ramp up global warming. Again, best to have supernatural elements on our side, and the White Council would likely be one of these.
Death Masks? That would have been pretty easy with a bunch of clued in mortals. In fact, I doubt the Denarians would have even tried something so public like stealing the Shroud (which would have sent supernatural warning bells off all over the place with a clued in populace). If he had, he'd probably end up dead.
Blood Rites would have had investigation with as soon as the abnormal deaths started. Local authorities would know something was up with that if they knew about magic. Overall things would have been resolved sooner.
Dead Beat? Cowl is powerful and all, but it's going to be hard to pull off a ritual like that if there's significant military intervention, which would have happened. Being vulnerable during the swallowing stage would have led to his death from massive long-range fire. Certainly the zombies wouldn't have been an issue. Again, ghosts and the like are potentially problematic, but IIRC now, if they acknowledge your presence you can hurt them, and there are other ways that anyone can do such as magic circles. Overall, a serious threat, but a lot less serious with mortal intervention.
Proven Guilty....hmm, well, for what it is worth Fae in general are the easiest thing to take out with steel jacketed rounds. So generally they wouldn't be a problem, I don't think. Fewer people at Spattercon would have died, imho, since it would be recognized as a potential supernatural problem quickly, and confirmed if they accepted wizard-help.
Err, getting tired of doing this. I'll go to Small Favor. The archive would never have been taken. She'd have 24 hour protection and possibly a small army protecting her at all times. She's that important and I think everyone would recognize that. Consider how much help Marcone provided with ONE helicopter. Now imagine full military support on the island.