Quick take on the match from my pov:
I can completely understand why he resigned. My guess would be, that he didn't want to lose without putting up a fight at least (which he couldn't) so he decided not to lose by retiring.
I believe he did this for two reasons:
1. To prevent his teammates from being discouraged.
Think about it: The tie could have gone both directions and no match was certain to go to either country, so all players must be quite tense, knowing that they don't have a save win (f.e. Wang/Huang in the Sudirman Cup) later on.
SYQ was completely demolished in the 2nd set, I am sure this would have given a big morale boost to team Japan while China would have lost morale on the other hand, especially considering how well they played against Japan in the Sudirman Cup final.
To prevent that SYQ decided to retire the match, after everything stopped working for him, to give an excuse for losing the game.
There is a huge difference for losing due to an injury and losing because you play horrible and a devastating defeat would have been worse for the morale of the remaining Chinese players than a defeat due to injury.
2. SYQ waited till KM's matchpoint, in case KM would have an injury, that is why he did not retire earlier during that game (according to the translation of SYQ's words by a commentator under the interview on Badminton Europe).
If this had been any other tournament, I am sure SYQ would have retired after the first game, or at the beginning/interval of the second one. He waited till matchpoint, not because he feared losing to Momota, but because he hoped for any chance to get a victory for his team, even if it caused a shitstorm.
And if this was the case that SYQ waited till matchpoint out of hope of winning (however small that chance may be) and not to discourage his teammates/encourage the Japanese team, it would make no sense to be honest about it in the post game interview which his teammates/opponents may hear.
Morally this was more than questionable, but I think you guys shouldn't go too hard on SYQ for doing what he did today.
Hope he will be able to play tomorrow. Ginting looked really nervous today and scored more points than VA

.
He may start to crumble before SYQ does, can't really see LGZ having a chance to win that matchup...