Leaving aside the whole railroad debate...Sorry, I just don't see it that way. His proposed choice of action - flee from town after being accused of a major crime - was going to result in him being out of the adventure for the foreseeable future.
I think that there could have been a mismatch in your preferred DM style vs the actual game that was being run. You want to present the players with difficult situations, but not give them hints as to how they should respond. That sort of DM style meshes well with sandbox-y type games where there's little to no script, and the players' actions (or reactions) are the driving force. It doesn't so mesh well with prepared adventures, unless the DM is willing to chuck the adventure out the window and go off-script.
If there's only one possible scripted adventure and it's right there and only there, then the players have to be aware of that in some fashion, whether you're giving them hints or you tell them up-front or whatever, so that they can work with the DM to stay within the bounds of the game. If you present them with what appears to be unscripted freedom, it's a bit unfair to complain when they try to exercise it. If you want them to stay within the adventure, then you're probably going to have to lay down some heavy clues to show them the way.