While I had problems with Scotty's characterization in XI, in particular downgrading him to a comic relief role, I had no such problems in STID. Taking a stand in what he believes and willing to resign in protest of a mission he feels is wrong is perfectly in character for Scotty, and I could easily imagine Doohan Scotty doing something similar.
I do wish they didn't go in the route of saying he objected to a military mission because Starfleet isn't military. They could have just said he had problems with the mission and not opened that can of worms. But whatever, "Starfleet isn't the military" is a lie that existed all the way to TNG and for whatever reason Abrams wants to continue with it.