Regarding to theory that Eteri simply replaced Alina with 'better' and 'newer' product of Factory...
Assuming we don't believe theory according to which Alina is a brainless barbie doll who is manipulated by evil Eteri and every her statement is in fact written by Eteri to mislead people and put few things into perspective everything fits the picture.
First,Eteri made it clear that for her, the medal you won ceases to matter after you take it off your neck and after that you need to work like you never won anything. Alina had 2 very hard seasons both mentally and physically, she said that after last season, she wanted to relax a bit and was tired of competition, do we have any reason to believe she is lying?
So at the end of last season,we had a situation in which, Alina wasn't ready to work 'like she never won anything', was under a coach who demands exactly that and leaving her,at least back then was out of question(simply, it surely doesn't make her chances to win better) and she probably doesn't want to take full year off due to several reasons (first, she needs to win right to compete in 2 GPs next year, second-she has many contracts and her sponsors probably want her to be active).
As far as I know, either Eteri or Alina said that Alina was told 'it's up to you if you train, you can stay away from training if you want' (something along these lines), what is the easiest explanation of that? Imagine if Alina walked into Sambo one day and told Eteri "I want to take it easy for next season,then we will see", what do you think Eteri would answer? Most likely something like-"Sure, but if you aren't doing 100% don't expect much of my attention,I have army of hungry girls to think about".
If you believe Alina, Eteri's rumored words and her rumored 'lack of attention towards Alina', also her willingness to let Alina take part in so many shows and everything else becomes easily explainable and true to Eteri's style (she isn't going to lose much time on somebody who isn't giving her all to training,regardless of who she is).
I think that both sides were happy with that arrangement and Alina was okay with having as much attention from Eteri as say, Moris, until GPF happened. Alina is of course experienced skater who has tasted defeats but... there is a defeat and then there is a hopelessness, she has lost before but she has never been in a situation where she needed borderline miracle (her best performance and one of 3As worst performance) to win a medal,nothing to say about the fact that Even miracle wouldn't be enough to get her gold. This may be fine for Moris for whom as rumors have it, figure skating is a never ending party, but for 'champion of everything' such state of affairs is probably very unpleasant.
At some point it hit her hard that... while she was partying, her team mates were studying the blade

and she had little to no shot at beating them (all of the 3A improved dramatically during the Season,Especially Anna and Alena),this makes her change of 'fighting spirit' after JO and open skate very logical and explains her decision to miss Russ nats.
All you need is to believe Alina (and she definitely deserves that much respect) and everything that happened sound less dramatic,considering that it's 17(!) years old we are speaking about.
it's Alina decision, she needs to decide what does she want, to me it's clear that she doesn't want to 'just skate', she wants to have a real shot at winning and I really doubt she will leave Sambo, Alina Better than anybody knows that Sambo is a place where winners are created and you won't win anything with running away from Eteri. It's matter of how much does she want it, she said that she no longer wanted to work from 6AM to 9PM, Soon she will have to finally decide if she does want winning again bad enough that she is ready to work like she never won anything, if she decides to try it again, then there is no place better than Khrustalny for that and no coach better than Eteri and most likely that will stay that way for a foreseeable future.