Haha what? None of these make any sense. Samus is a disciplined warrior and the need for a hierarchy during missions is certainly important but she is under no obligation to work within that hierarchy much less be on, as this game portrays it, the lowest ring of it. Given Samus' abilities she should be at least on equal footing as Adam. The point being though, that she's an independent. While this may be a joint operation, she has no obligation to any of the soldiers nor Adam, their military conduct, or regulations. Especially if her life is jeopardy for whatever reason.
Ridley has died and come back many times, this is a non-argument. Not only that but the game can't even go out of it's way to explain WHY Samus has that reaction to Ridley at all. So unless you know what happened from previous games, all you get is her freaking out at this one giant monster but not any of the others in this game. Even by it's own rules it's not justified.
Oh please, first off as others have mentioned Samus has displayed how she feels in other games when Ridley inevitably reappears. Secondly, even in older games if this was an issue they could easily animate it or find a way to make it apparent that something is wrong. Samus suddenly getting down on one knee or starting to slowly walk back then trying to run away or making it so the player can't fire at him in the beginning of the fight while he approaches her for some reason. It doesn't always have to show her face and make her talk to display her emotions. We'd easily be able to infer her emotional state from such things, none of which happened in other encounters with him..
Samus being a mercenary doesn't make the laws of the Federation she is a citizen of not apply. Her only options were to follow orders or leave.
Also, although it's questionable if Other M and the Prime games take place in the same canon, even if counted Ridley does not die in those games with the finality of his death in Super Metroid. He always fell off camera. In Super Metroid Samus obliterates the entire planet his body was on. She makes it clear in the opening cutscene that she is confident that he is dead for good this time.
People also overblow her reaction. It lasts about one minute and she doesn't turn into a crying girl. She screams "Ridley?! No, it can't be!" And stares at him while remembering what happened the first time she met him when she was 3. She snaps out of her flashback just before Ridley grabs her and actively tries to break free when he does.
Metroid: Other M - Samus going against her character by turning to shoot the baby Metroid and Adam stopping her.
I wouldn't say this is against her character. She hesitates at first because she remembers the baby Metroid that saved her life. This baby metroid is different, though, because she wasn't there when it hatched and therefor it didn't imprint on her. She probably realized that or just decided that it wasn't worth the risk since the last time she saved a metroid it caused the problems that she needed to be rescued from. She turned out to be right, since it does try to attack her.
Wrong. The plot of the game is to rescue the baby metroid which was stolen from the Federation labs. Now her going to rescue it could have some feeling involved about caring for this creature, however, I want to note that the question here is whether she cared about it like it was her child. The space pirates and Ridley/Mother Brain by extension are assholes as has been shown before. They are going to treat the creature horribly and try to use it somehow to bolster themselves in someway or another. The "feeling" here could be: 1) To stop them after they stole something which could potentially make them stronger 2) To stop them from mistreating the last animal of its species. So the reason for the rescue isn't some I can't live without the baby level thing but to stop what could be developed by an evil organization after studying it, something the Federation would do as well but that's beside the point.
Honestly, she's still pretty cold towards the baby metroid considering what it did. She talks about it pretty matter-of-factly. She's grateful that it saved her and a bit bummed that it died, but she doesn't act like it was her child. The feeling I took from it was that the whole thing made her kinda question her actions, since the thing that she dedicated her life to eradicating saved her life.