As you yourself noted she didnt skate badly at Skate America. It wasnt even a good event either. Yet she finished 9th with by far the lowest PCS of the field, much lower than some international journeywomen who had hard falls and completed less triples in their LP. At this point ending her career with a 9th at Skate America would be the most respectable note she could hope to go out on. Anything to come would be only worse, maybe ending with a 7th at Sectionals, a 12th or worse at Nationals, take your pick. She isnt even likely to ever get to compete at a grand prix event again if she continues, so ending it even being on the stage at an event of that caliber is already something she would be unlikely to be able to improve on at this point. In reality she would have been wise to end it with her great performance and 6th place at Nationals in February. EVERYONE expected that is what she had done, the crowd gave her a wonderful goodbye ovation, she reacted with tremendous ovation and appreciation as if it were a goodbye, then she comes back, and it is like "what the heck". Apparently the judges thought this too and showed with their very harsh scores (even considering her diminished skating quality, slowness, lack of a triple lutz, etc...) they are ready her to retire as well. I doubt the reception will get any kinder in the future.
I assume Fumie Suguri is retired now. However by the time she was essentialy forced to she had slipped so far down in relevance she wasnt even competing at the National level anymore. Most people probably dont even know what her last competition was. That is not the way anyone would want to go out, and Flatt is dangerous close to the same fate already. Or should I say was close to the same fate. It appears this is basically an early retirement announcement so she has come to her senses and will save herself the ultimate embarassment the 3 time World medalist Suguri set herself up for. Good for her!