Re-watching "Advances, None Miraculous" and "The Whores Can Come", I had two mains things on my mind:
1- John Hawkes never ceases to amaze me. He's so expressive without overacting ever; he can convey so many sentiments that it's incredible. The look in his eyes can be so bright, so innocent, so clear...but also so blank and dark sometimes. Here I'm thinking of that killing scene at the end of "Advances" when he sees Seth stepping outside, understands that William passed away, leaves Trixie and Jewel and just walks in silence in the thoroughfare, wearing death on his face and in his stride.
2- I came to the conclusion that Sofia, although she's also a little girl, is the most metaphorical character in the show. Deadwood is often described as realistic because it's based on historical characters and events, because it's grim and gritty, because of the credits' puddle of water where mud, blood and shit mix up...but it's merely mythological.
It is the story of beginnings with titans, gods, giants and leviathans; it's the tale of how civilization begins, how human individuals come to gather into a community; it's the childhood of a human society ruled by laws and regulations, but also by empathy, solidarity, compromises and interdepedence .
Sofia embodies that idea with some "meta quality" added in the mix. She metaphorically represents the camp as it's changing under our eyes, and the camp that is watching itself through the other characters whom Sofia keeps observing.
She's first introduced as something of a mirage, some hope that might come to happen, close enough for Jane to notice her but kinda elusive, about to disappear. Yet she survives the violence that kills her whole family and later Bullock saves her from the wolves. In a way Sofia is born out of chaos, and her early journey/trial represents the struggle between aorgic(infinite possibilities) and orgic or organic (organizational system, order), to use Hölderlin's words. In season 1 she's mostly mute until she finally voices her name: Sofia. It's a pivotal moment, in which you can see that culture might overcome.
Sofia's progresses, as she grows and learns stuff, mirror the camp's,a camp that starts as a lawless place to evolve into being part of the United States. BTW even the "Chinks" in Deadwood change...season 1 Mr Wu knew about three words of English while season 2 Mr Lee speaks fluently and says about himself "I'm a civilized man".
Sofia is first protected, taken care of, and tutored by various Deadwood characters, but by the end of the season 2, she speaks English, she's no longer Alma's ward but her adopted daughter (the scene with Richardson in which Alma calls herself "her mother" is very significant) and Ellsworth is becoming her other parent (and again it's meaningful that Alma tells Trixie that she's delighted at the idea of Ellsworth being Sofia's father...not the father of her unborn child!). Meanwhile Deadwood is about to be annexed, to join Dakota's bosom.
There's an obvious parallel in "The Whores Can Come" between Alma finally accepting Ellsworth's proposal (while he's carrying Sofia!) and the deal that Al strikes with Jarry, and, through him, with Yankton.
So, apart from The Pinkertons hate, it makes sense that Al sided with Alma against Miss Isringhausen, for Al and Alma are both the godlike figures of the camp, very self-centred at first but eventually providing for the community (yes I still think that Mrs Garret-Ellsworth is a sort of Alma Mater for Deadwood and a mother figure when it comes to the little girl), working for a common cause. They are the mythological parents of Deadwood, and even though Al's first instinct was to kill the child -- like gods of old or Titans, I'm looking at you Kronos!(and Kronos was the most aorgic force in Greek mythology unlike Zeus who was pure orgic!) --, he ends up protecting Sofia in season 3.
In "Advances" and "The Whores Can Come" there are many quiet scenes, in which the viewers can see that William's fate has sort of silenced the whole camp, it's enhanced at the Gem or in the final street scene of "Advances", or during William's funeral. So of course when Trixie visits Alma, she points it out saying that Sofia has been quiet since the boy's accident.