Why is it when one player does something that disrupts the game like taking off and fleeing instead of trying to work out the issue of being arrested
Taking off and fleeing
is one way of trying to work out the issue of being arrested. Given that the arrest is for a crime that the PC did not commit - and is, therefore, in some sense wrongful - what reason has the PC, or the player, got to think that justice will out in the end?
this is a game and one that you play with other people and sometimes you need to take that into consideration when making character decisions.
Well quite. Whereas, in this situation, it seems that the other players, as opposed to having their PCs back the PC whom they knew to be wrongly accused, decided to hang their fellow PC - and thereby their fellow player - out to dry.
The players want to do something. He wants to do something else, which includes abandoning the party and their ties to the town they're invested in.
Who talked about abandoning the town? Plenty of fugitives flee from the law without abandoning the town. They hide out in the woods. They sneak back in at night. Their friends sneak food and water out to them. Etc.
How is he not being the game-disrupting player, in your mind?
Because he is the one whose PC the GM has had wrongly accused of a crime, and when he responds to that by having his PC try to flee - a fairly common and reasonable response to unjust accusations from unknown authority figures - the other players, as I said, hang him and his PC out to dry.
Because becoming an outlaw is not something that the other players wish to do?
Neither does the player, presumably. But nor does the player wish to have his PC arrested. The situation seems to have been contrived by the GM, and then when the player tries to deal with it, the other players shaft him. What do they think they are adding to the game at that point? What was the GM hoping to achieve?
As I said before, the guy is trying to run Runelords not Cops or the First 48.
The GM serves to create the background, the scenery, the supporting cast, the antagonists
And apparently the plot as well. If Rise of the Runelords only works if one of the players - who is playing a brigand, as apparently okayed by the GM - lets his/her PC be arrested, the GM might at least have the courtesy to explain what is going on, and even to treat the whole thing as a cutaway, rather than presenting it as a genuine situation in which the player has genuine choices to make for his/her PC.
Because his PC is innocent of the crime he's accused of?
Because the other players know this?
Because even though the other players know this, they all decide to proceed as if the accused PC is guilty? Even though, at that point, there's been no corroborating evidence either way.
The accused PC is falsely accused of crime, and then finds the rest of the group siding with the NPCs. I'm not sure how anything he does at this point could be considered "disruptive", once the deck's been stacked against his favor like that.
This is exactly what I was talking about.