Alina got passed by all three of the 3A because she had an off day - with two falls and only 5 triples - and they did not. This is only the second time in her senior career that she's had what can really be called a bad skate, so it would seem a bit premature to call her done or doomed.
Her skating skills have not deteriorated at all. There's a video - here:
https://www.youtube.com/watch?v=mWKpcMLdIc4 - in which Alina is fully able to complete the entire course. Others that they asked to try weren't able to. If she had poor skating skills, she couldn't possibly have done this.
How can we say that her team doesn't have her best interests at heart? They've given her programs that will take her to the top while still being in her range of capabilities. They've been there for every setback and every challenge, and haven't given up on her since she came back to Eteri. She attempted a quad on a harness, yes, but that doesn't mean that they want to put it in her programs or that they think she should do it now. They know that that wouldn't make sense. Team Tutberidze has said that they limit quad attempts and take safety very seriously. I believe that, and we don't have any reason not to. They took out Alena's 3A and Anna's 4T, for example, when it became clear that it would be best to stop on those jumps for the time being.
Alina has been successful both this season and last. Silver is not a loss, and the occasional podium-miss doesn't mean she's over. Russian Nationals is quite possibly the hardest competition to date, in terms of caliber. Never before have 10 skaters scored above 200, afaik, and certainly not at a national championship. This is to say that 5th at Russian Nationals isn't a sign that she is doomed. It shows the depth of the competition, instead.
And Alina, on her worst day of the season, still scored well enough to place above 13 skaters at such a hard competition. That's pretty danged good, and I'm sure she's learned just as many lessons from that day as from her free skate in Milan. It's the failures, in addition to the successes, that help us as humans learn, and it's no different for an elite figure skater. She's just 16 and has many more years ahead of her, with plenty more to show the world, that it definitely is not time for her to move on. (unless it's her own choice to leave for her happiness and health, of course). One doesn't have to be a fan of Alina to realize that one bad day doesn't mean she's done, and I know that Alina will follow up on Russian Nationals with a great skate and score at Europeans