Nah, the fact that Sean ran is a big problem because even his character fails to adequately explain it, and the topic is brought to his attention multiple times. Also, bear in mind this wasn't just a reflexive thing, they committed to running away for a long time. You could say that past a point Sean & Daniel are "all in" on running because they do commit legit crimes after a bit. But still, there's plenty of time before then where Sean had ample opportunity to second guess his choice. Also, there's stuff like Brodie -- who is clearly framed as a moral character/ "road guide" -- saying that running is a good idea. Which couldn't be further from the truth, it's the worst possible thing Sean could have done.
There's just no way they would have been blamed for the initial incident and if Sean had any sense at some point he'd realize that. It's literally an unexplainable, freak accident, that blew up half a suburban block for no reason. A decently smart 16 year old kid eventually would think "wait a minute... what could they actually pin on me? are they gonna guess my kid brother has super powers?" The best motivation Sean musters is that he was afraid that him and his brother would be separated but that's really weak. Even his grandparents straight up tell him there's no way he could be sure of that and they're right. Fleeing the entire country on a baseless hunch is really stupid.
Funnily enough the cop at the end of the game straight up says they would just have been given to their grandparents after the initial incident. Which is what I would have assumed. I think most logical people would have assumed the same thing. That's a problem when one of the main character's core motivations required him to be extremely illogical for long periods of time, despite other characters telling him better. Sean isn't framed as being unintelligent or irrational enough for that to make sense. It just happens because it has to. That's a fair criticism.
I think part of the issue here is you're taking Brody and maybe Sean as voices of the author and not the flawed people that they are in this story. The other is that I don't think that you're not giving enough consideration to Sean's age, new circumstances that arise past the point of running and other motivations Sean has for not turning back. Sean's age is especially a factor as teens in the modern age think relatively small things to an adult like getting rejected by your crush are life ruining, some will act out and/or run away from home for these relatively minor things.
So in just the initial situation post their dad's death and Daniels psychic explosion, here are some things to consider from Sean's perspective, some he brings up himself to some extent or another :
-a cop just unjustifiably fatally shot his dad just because he had beaten up a kid his own age, it at most looked like a possible stabbing but no weapons were visible, and no further blood was spreading to indicate a serious wound. His faith in the police to act rationally has just been shattered, and in the moment he has every reason to fear they might act violently towards him and his brother, with a cop car flipped over and a cop seemingly dead/seriously injured.
-even if they aren't violent towards them, he at least has reason to think that at minimum he goes to juvie, at worst to prison. Again, his faith in law enforcement being just has taken a huge hit, so even if logically he thinks that they can't be held accountable for it, there would be doubt that they wouldn't try to pin it on him somehow. Even if not legally held accountable, the court of public opinion is going to be brutal towards him as well.
-Sean is not just running away from any kind of punishment he thinks will happen, but from confronting what did happen which is only heightened by Daniel not remembering. Confronting his dad's death, possible separation from his brother, possibly being without a home if his grandparents don't take them/him in, even if they do starting over in a new place with his involvement in a freak accident that killed a cop hanging over his head. It's easier for him to just pretend they're off on a hiking trip early then face the weight of the reality that awaits him if he surrenders himself. To add onto this is the political climate the game is set in, with the basically Trump candidate in the game spouting racist rhetoric against his race.
Then there are factors that come into play later:
-him running in the first place makes him look guiltier than he otherwise would be, so that plays into his mindset
-Daniel's powers emerging. While it's not like the cops are going to link what happened there to psychic powers as if they're omniscient, Daniels powers aren't bound to go away either and to Sean's knowledge appear beyond his control when highly emotional. There is a feasible chance that something could happen that could get him taken and experimented on. Beyond that, it helps Sean rationalize his own decision to run away from the entire situation if he can make it about protecting his brother.
-his encounter with the gas station owner further breaking his trust in most adults/the country to treat him right and adding to what crimes can be pinned on him
-Brody doesn't to my remembrance push him to keep running, but given how he lives his life is supportive of it if that's what Sean chooses. Without his help they might well have just gotten caught or given up from lack of transportation/supplies so he plays a significant part in their journey, but he himself is shown to be flawed if you keep up with his posts on his site. Brody is kind of how I imagine some REE members would be if they matured some and chilled out. They disown their families but Brody makes peace with his in the end, and acknowledges that someone like him is useless at important things like managing finances. That he appreciates/admires his brother's stability in taking care of the family, despite their political differences.
As you say, multiple people in the game criticize Sean's choices, and while they aren't the ultimate authority and have their opinions steeped in their own biases, the game in the end leans towards their viewpoint I think. While there is no given "good ending" by the creators, the separation ending is the one that best fits the bill. If you teach your brother right, even if you choose to escape to Mexico, he chooses to stay and face any consequences. Sean in a lot of ways made bad choices, that in the end led to the best choice for himself being a new life elsewhere. This is the ending I got and was satisfied with it, and oddly proud of my fictional younger brother for having learned the right lessons.
Sorry for late response have been busy. You bring up good points and I can see how you could view things the way you do, but it's not the impression I got. Life is Strange 2 isn't always solid in explaining rationale which is one of it's faults, unless you have a similar mindset to what they're going for some things could get muddled. They're French developers who do research on these matters but that can only get you so far.
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