You know, I appreciate the notion that there are people amoung Kirk's crew who wouldn't want to come along for this mission. That feels real and I like that they tried to include that. But at the same time I think it would have felt more natural for, say, Chekov to be the one to disobey. He's young and isn't as rigidly indoctrinated by the chain of command as Scotty ought to be.
What about Scotty's character in the previous film gave you the impression that he was "rigidly indoctrinated by the chain of command"? His testing of dangerous and unproven equipment on a famous admiral's prized pet? His exile to a frozen wasteland? His assistance of a fellow Starfleet exile to get back to the ship he was kicked off of, no questions asked about the reason he was stranded there? His refusal to immediately answer Spock's question about how they got aboard the Enterprise despite Spock's superior rank? His colorful responses to commands from superior officers or bragging about his transporter prowess in their presence?
Seems to me that refusing to obey an order that's immoral in his opinion or could endanger his beloved ship and her crew for the wrong reasons is right up Scotty's alley, in either universe. He was never afraid to go against orders to do what he felt was the right thing, as in the previously mentioned sabotaging the Excelsior and stealing the Enterprise to retrieve Spock or sneaking in to Klingon space to rescue Kirk and McCoy from Rura Penthe examples. Even the most innocuous and endearing aspects of his traditional behavior exhibit his unconventional nature: his multiplied by a factor of four repair estimates, for example. Someone who was rigidly adherent to the chain of command wouldn't deliberately mislead them about how long he thought it would take to fix something; not even jokingly. Or his choice to fight the Klingons on K7 against Kirk's orders not after they'd insulted the Captain (which he ordered Chekov to not respond to), but after they'd insulted his ship.
