I guess I can understand why her sudden appearance would be off-putting compared to established characters like Molly.  I dont mind it as much because I like when these sorts of stories (especially ones that have gone on as long as Dresden has) remind the audience that there is a lot of other crap happening out there in the story-world, so that Significant things dont always have to happen near the Main Character.  Some of my favorite stories made their fantasy world seem so much richer simply by mentioning other events or legend or whatsoever entirely in passing.

I also didnt come down on the anti-Susan side of things, so I actively wanted Susan to come back and be relevant again.  She was either actively participating or else was a primary motivation for all the the first five books, then wasnt mentioned again beyond the Other Ex that Ended Badly for another seven. Saying she dropped off his radar on purpose to hide their love-child from his horrifically dangerous lifestyle felt realistic and thematically interesting in the sense of highlighting the difficulty of the morally grey.

I see the pattern somewhat repeating itself with Murphy,  no longer in law enforcement, while not old, getting past the age to go one one one or even to be part of a team against the kind of enemy that Harry is facing these days... Now debilitating injury on top of it...  I know her die hard fans will settle for her being a port or perhaps some super computer sleuth, but face it, that isn't the Murphy that endeared herself to us..  Perhaps that is how it will play itself out, Murphy will voluntarily remove herself from the picture.

He already did Susan the Dinosaur in Dead Beat. Harry commented that he took the T Rex's body when he could have done so with any of the zombies.

I think you mean Sue...  But technically she was zombie animated at the time by Harry's spell.   I think it possible, but it might break more laws of magic and nature than even Bob would be willing to break.

This is actually more what I would expect, something along those lines.  Not necessarily exactly that, but simply killing Maggie is too easy, too quick.  From revenge, it would probably be more interesting and more manageable to somehow corrupt or taint Maggie.  Ideally, from Nicodemus' POV, that creates a situation where Harry must either kill his own child (thus in Nicodemus' twisted thinking equivalent to him and Dierdre) or live with the knowledge of what she has become.

 Harry having to kill Maggie would be a cruel twisted thing that Nic would love to arrange..  I think he might take it a step further, have Maggie sacrifice herself willingly for Harry as his daughter had done.  If Maggie had to be "put down" because of what she had become, Harry maybe wouldn't forgive himself but as seen in a mercy light learn to live with it.. Sacrifice herself though, perhaps like her mother, I don't think he could.

But wherein Murphy is apparently the worst, surely her ceasing to be Murphy would only be a good thing.

  Really?  If she is no longer who she is at her core being, that is the problem, circumstances are now preventing her from being what she is..  She isn't a good listener,  if that isn't fixed this port in the storm role isn't going to work, she isn't going to be content with that kind of role.

Really?  Mab could literally have ordered Harry to get her the Sword and he'd have been powerless to stop it.  Even without Mab's orders Harry was under the Mantle's influence.  He was so terrified about the Winter Knight Mantle he chose suicide.  If Harry was willing to have himself killed because of the Mantle why would Murphy trust the Sword with him?
 Murphy's judgement was correct that a Sword may be vulnerable under such circumstances.

Not talking about Mab and the Sword...  Oh Murphy was correct that the Sword was vulnerable but then she went ahead and did exactly the thing that made it vulnerable... But that isn't the point,  the point is she is clueless about the post Changes Harry... She wants him to return to pre Changes Harry, that man is dead, she is afraid of the post changes Harry..  Does Murphy even realize that Harry suicided to avoid getting the Winter Knight's mantle?  Or that he is on first name basis with an Archangel?  Well, she might now..

The Sword worked perfectly for her up until Nicodemus surrendered.  She was in the right up until that moment where emotion overran reason.

No,  for the record her ovaries had nothing to do with it....  Love had nothing to do with it..   The Sword is meant to fight Denarians, but if the Denarian surrenders, then he/she is allowed a chance to seek a path to redemption..  Murphy says up front before the fight began, before that anyone knew she had the Sword concealed in that tube, that she didn't believe in redemption for Denarians..   What broke the Sword was her condemnation of Nic, the "damn you.."  Judgement is for God not Knights..

Quite a judgement being made there

Only quoting or paraphrasing not just Michael's words, or Uriel's words, but Murphy's own words... 

No such thing as too many people to love

True, but she isn't indispensable,  Harry has many friends to turn to for love and support is the point..

As a fan why would I prefer her to die? 

If she ceases to be Murphy you might....  If she goes too afar a field from what she originally was..  When the book is perhaps more readable without her than with her... Or it doesn't matter if she appears on the page or not..

As for Murphy not really being meaningful for the stories, that's up to Jim.  Louis Lane didn't have powers but to Superman she was his rock, his port in the storm.  Murphy's meaningfulness might be less about her fighting ability and more about being Harry's port in the storm.

  But in the Superman stories once Superman grew up he and all those around him seemed to freeze in time...  The never aged from Jimmy Olsen to the guy who ran the newspaper, so MS Lane as the perpetual perky inquisitive foil remained plausible.... More or less...  Susan was good in that role until it got serious between them and then seemingly Jim had no
where to go with her, even when she became a half turned vamp, which could have kept her interesting..  While Murphy might remain meaningful as Harry's port in the storm, she isn't his only port anymore..

Jim may have meant it as a joke, but even joking about it says it is on his mind..

I guess it's Michael's time to die as well.  Not every character needs to die when they aren't ready to be on the front lines fighting.  I think what it's showing is just as Harry has outgrown his enemies of the past, he is now getting to a point where his allies of the past just aren't up to fighting the fights he's going to be having...  Marcone, Murphy, the Alpha's, Thomas....  They just aren't on par with Harry anymore, he's too big just as the enemies he's going to be facing are too big.

True, most know perfectly well they are not on par with Harry, but Murphy doesn't...  That is the point, she thinks she knows Harry and what is best for him, but she is in fact clueless about him, this is what made  her a liability in Skin Game to the point of disaster, i.e. the breaking of a Holy Sword..  Someone earlier spoke of setting up what is to come in the next books...  I think we are being prepared for her exit, whether it is a mere break up or something more lasting..  I also think if her role is diminished from being someone who physically fights at Harry's side to some "emotional port in the storm," not just fans in general but her fans will be disappointed..

   I seem to recall a "Tweet" from Jim maybe a year ago give or take that he was  emotional after writing Murphy's funeral...  It created a bit of stir here of course.  The question is, was he really or just pulling our legs?