Ok so let's think of the favors Lara could've done.  One thing that comes to my mind is helping to defend Demon Reach.  If that's the favor, then Winter owes Marcone a favor too since his forces helped defend it too.

I think one of the favors might have been Thomas assassinate some one.

In chapter 6 Harry talks about the amount of influence Lara is gaining in the government.  In Jury Duty, we meet Tania Raith, a low level DA, who could exert influence over DA's higher up in the food chain.  Mab may want to use the mortal authorities and Murphy as leverage over Harry.  Perhaps Lara helped Mab get that influence.   

Another thing that i found interesting was this:
"“New colors,” she said, her voice velvety smooth and calm. “The shield used to be blue. What changed?”

“He made an alliance with a powerful guardian entity,” said the second monster, a woman seated beside the first. She was as lean as a rod of rebar, but colder and harder, and her opalescent green eyes were too big to be strictly human. Silver‑white hair fell to her shoulders, today in a fine silken sheet. Her voice sounded calm and precise, and she wore a glacier blue dress that belonged on a runway. “It does not interfere with his duties.”"

That exchange between Lara and Mab makes me wonder how Harry's relationship with demon reach has changed him, and to what degree Harry can use power from Demon Reach when he isn't on the island.

Mab also implied that Lara would like how Harry tasted and remind her that Harry was a member of her court.  When Harry and Mab had sex to seal the deal for winter knight she said that Harry was hers.  I also think Bob may have mention something about Harry kind of being married to Mab.  I wonder if Mab protects Harry from being eaten by a wampire.

G33k: Fight Night, I like that. 

Murphy would never willingly take up a coin, and she is willing to die if it helps defeat the nickle heads.   

Harry blames himself for everything, so i could see him making a deal to get Murphy healthy.

I don't think the issue of Murphy injury should be solved quickly. 

Dina: I was thinking about that too. 
Arjan: While Harry and Marcone aren't friends, Harry has no reason to want to little girl to be in a coma.

My best guess is that Harry either forgot, or couldn't find a way to get to Marcone that would keep the girl's existence a secret. 

Murphy may end up continuing to live with her injuries.  It happened to Micheal.  It would cause more emotional pain for Harry since he would end up seeing her suffer through recovery and set backs just a like anyone else.  People do end up regaining more function than doctors estimated from time to time.  If you think about it, as a doctor, its probably better to low ball the recovery estimate, to keep the patient from having false hope.   

Also at the end of Skin Game, didn't original doctor giver he a better prognosis?  I think Harry told Micheal that the doctor said she could get back to 90%. 

She might make out ok enough to be more than functional.

Lastly, Murphy won't make any deals to heal herself, but I think that depending on what the offer is, Harry might take a deal to make her better.

You know, there is a possibility that we aren't talking about.  Jim has hinted that the government has at least a clue of what's going on.  We've seen evidence of this in Dog Men.  Maybe the feds are pushing the investigation, so they can make Murphy an offer she can't refuse.  Come work for us and this investigation goes away. Maybe Uncle Sam can hook Murphy up with a clinical trial of stem cell treatments for her injuries.  This idea would be cool because it keeps Murphy a vanilla mortal, brings her back to something like law enforcement, and it could add more tension to Harry's relationship to her and to his relationship with the council.  It might even fit the funeral line, what if her new job is so secret that they fake death. 

I didn't think that Harry and Murphy suspected that Rudolph worked for Marcone.  It was pretty clear in Changes that he was unknowingly working for the Red Court.  I suppose Rudolph can just be generally corrupt and work for the highest bidder. 

I have a few ideas about who might be behind this. 

We know of two people who have influence in local government, Lara and Marcone.  We know Lara has a relative at the DA's office, Tania.  Marcone probably has a DA on payroll too.

Nicodemus would know where to point the cops and has reason to go after both Harry and Murphy.

Mab, would also know where to point the cops, and isn't above blackmailing Harry to do her bidding.

Mavra, has used pictures of Murphy to blackmail Harry in the past.  I don't know how she would know about the bank job, but it is possible.  It's kind unlikely because Harry knows Kemmler's method of dealing with the Black Court.

Lastly, given what Ebenezer said, someone working for either the white or black council.