Receipts to support your points (also from Jedi Apprentice 5: Defenders of the Dead, the first book in the Melida/Daan arc):
"How did you blow the deflection towers?" Qui-Gon asked Nield and Cerasi curiously. It was a question that had been bothering him since he'd heard the news. "You'd have to hit them from the air. But floaters couldn't do that job. You'd need …"
Qui-Gon paused. He turned to face Obi-Wan. Slowly, Obi-Wan pushed his chair back. Qui-Gon heard it scrape against the stone floor. Then he stood. He did not fidget or look away. He met Qui-Gon's gaze.
"So it was you," Qui-Gon said. "You took the starfighter. You took it knowing it was our only way off the planet. You took it knowing it was the only hope for Tahl."
Obi-Wan nodded.
Cerasi and Nield glanced from one Jedi to the other. Cerasi began to speak, but thought better of it. The tension between Qui-Gon and Obi-Wan was private. "Please come with me, Obi-Wan," Qui-Gon said curtly.
He led the way to an adjacent tunnel where they could talk privately. He waited a few moments to compose himself. Bitterness had no place here. Yet he felt it surge within him. Obi-Wan had broken his trust.
He did not know what to say. His emotions swamped him. Qui-Gon recalled his Temple training with an effort. He would admonish his Padawan according to Jedi rules. First, he would describe the offense. It was the duty of the Master to do so without judgment.
Grateful for a guide, Qui-Gon took a deep breath. "You were instructed not to take sides."
"Yes," Obi-Wan responded calmly. It was the duty of a Padawan to agree to his fault without argument.
"You were instructed to be available to leave at any time," he said.
"Yes," Obi-Wan replied.
"You were instructed that Tahl's health was your first concern. Yet you endangered that health by taking our only form of transport on a dangerous mission."
"Yes," Obi-Wan agreed.
Qui-Gon swallowed painfully. "By doing all this, you not only put Tahl at risk, but the peace process on Melida/Daan as well."
Obi-Wan hesitated for the first time. "I aided the peace process -"
"That is your interpretation," Qui-Gon interrupted. "It was not your instruction. Your Master and Jedi Master Yoda had decided that Jedi intervention at this stage could only prejudice either the Melida or Daan, thereby sabotaging the peace process. You were told this. Is that true, Obi-Wan?"
"Yes," Obi-Wan admitted. "It is true."
Qui-Gon paused. He gathered himself to deliver the Jedi wisdom of the Master and Padawan relationship. How the rules had evolved over thousands of years. How the Padawan's pledge of obedience had nothing to do with power, but everything to do with the gaining of wisdom and the humility of service. How he was not here to punish Obi-Wan, or even to teach him, but to aid Obi-Wan's own journey and enlightenment until the day he grew to become a Jedi Knight.
As for reconciling modern sensibilities with Star Wars' treatment of children... I'm tempted to write a full essay bc it's a thing I'm passionate about, but i don't think my brain has the power for that rn so I'll limit myself to just the highlights:
"Childhood" as we conceive of it today is a very modern construct, and one that has a lot of limitations in its practice, application, and practicability
There's some genre stuff going on here that all star wars media struggles with to some extent; Star Wars was always intended to appeal to children as well as adults, and in children's media, children tend to be the characters going on adventures and engaging with the plot. Hence a large number of teenage protagonists in the expanded universe: Obi-Wan in Jedi Apprentice, Zak and Tash in Galaxy of Fear, Anakin and friends in Jedi Quest, Ahsoka in the Clone Wars, Ezra in Rebels, etc. etc. etc.
in order for children to frontline plot in media for young audiences, adults can either 1) enable shenanigans (Dumbledore, Gobber the Belch in HtTYD, etc) or 2) be incapable of preventing shenanigans, either by ignorance (the parents in Magic Treehouse, Secrets of Droon, etc) or powerlessness (Sally Jackson, Leif's parents in Deltora Quest, etc). They cannot protect, at least not completely. I think it would be really interesting to try to write a children's adventure/saving the world series a la star wars or deltora quest or whatnot in which the adults successfully protect the children from the plot; the part of me that says nothing is totally impossible says it must be doable somehow, but I can't personally come up with anything, at least in the last 8 or so years that I've been considering such a project and revisiting it whenever I have the time to try to come up with something
I recall reading something somewhere (great at citing my sources, i know, but if I find a link I'll throw it in here) about a conversation between Lucas and Filoni where Filoni was like "Ahsoka is a child soldier! She's going to be traumatized!" and Lucas was like "Ahsoka is a padawan. She's been prepared for this, and has the skills and abilities to do what she needs to do." And I think that's a bit of tension that lives everywhere in star wars, all the time, forever
I think it's really important not to forget that padme is 14 in phantom menace. "children" have had adult roles in canon since the prequels came out and reducing their agency is not a reading that is supported by canon
I'll make a separate section here for my personal conclusions, since no one has to agree with me on them, but my personal interpretation:
People exist on a sliding scale of capability, culpability, and agency. Everyone reaches different milestones in those things at different times in their life, aided or hindered in those developmental steps by their environment and personal temperament and whole lot else.
I think it only makes sense that the Jedi Temple would be a place that emphasizes cultivating agency and capability from a young age, so that when young Jedi become apprentices (which, in JA, happens at a pretty normal age for historical apprenticeship in most fields, actually) they would be prepared to act in the roles expected of a Jedi regardless of age. Just as a printer's apprentice would have tasks he'd need to do for the rest of his life as a printer-- sweeping, cleaning, maintaining the press, inking, typesetting, etc-- Jedi apprentices are expected to complete tasks that they'll need to be able to do for the rest of their lives as Jedi: negotiation, investigation, protection of the innocent, and, importantly, moral decision-making with an expectation of having considered the possible consequences of those decisions and chosen to accept those outcomes.
With that in mind, and the understanding that children do their best to perform to the level that they are expected to meet, regardless of actual capability, I think it makes a lot of sense that Obi-Wan, over the course of the Jedi Apprentice series and especially during the Melida/Daan arc, goes through experiences in which he has to make decisions about his own moral beliefs and then enact those moral boundaries, and has to learn what is in his control and what is not, and has to deal with the fact that while he made a choice for the right reasons and was able to do a good amount on his own, there are still consequences, both unintended ones and ones that he thought he had accepted but is now actually having to deal with. There is still broken trust that "sorry" is not going to be enough to fix, even though that very real sorrow goes to the very depths of his soul.
These are the kinds of decisions and consequences that Jedi deal with all the time, and if he has to grapple with them at a younger age than most, it's a result of his own choices, which the adults around him honor in order to allow him to cultivate his own agency. It's not just the Jedi; pretty much everyone he meets throughout the series expects Obi-Wan to act with the same moral authority as an adult, if not with the same level of reasoning. And part of that is going to be a genre thing, but part of it is also just... being a Jedi. Being apprenticed to a Jedi. Because a Jedi's trade is to steer the direction of nations planets, toward peace whenever possible-- but it's not always possible. And so an apprentice to the Jedi's trade is prepared, from the time they come to the temple, to perform the tasks and use the tools and make the decisions that are required in order to be an effective Jedi-- including decisions like "I want to leave this path and do something else."