I thought I'd take the time to mention that a while ago I watched all available footage of Before Crisis. It was the most boring, monotonous thing I have ever had to watch. Now I can watch other poor pieces of fiction and breath a sigh of relief because "at least it's not Before Crisis".
Oh? That's too bad. I love it. I mean, it's more of a story game, but I like the story. I like the idea of the characters and their different personalities and I like the way it does address interesting questions of morality. Although I red the script rather than watching the play through because it’s difficult to skip over the fights. I also enjoy reading game scripts. But to each their own.
As to that elephant in the room, I believe many Turk fans have thought about it. I think the existing canon explains things fairly well. Tseng acted evil in front of Aerith because he thought it would be easier for her if she could hate him and see him as purely evil. Kinder to be a monster than a good man who claimed to care about her but wouldn’t help her, and so Tseng acted evil for her benefit (Case of Shinra explains this).
As for Reno, I think Before Crisis shows a progression; the Turks weren’t always the people they are in the original game. By the time Reno drops the plate he’s become a darker character. However, I think Before Crisis explains why the Turks couldn’t refuse the order perfectly well.
The President was going to kill all of them and the only thing that stayed his hand was Rufus personally vouching for the Turks. Of course, that doesn’t mean the President trusts them fully, and everyone else on the board aside from Reeve wouldn’t mind seeing them dead (Scarlet especially is probably still out for their blood). Any further insubordination while the President lives could mean the end of them.
So what? Die rather than carrying out the order? What good would that do? Shinra Company wants the plate dropped, the plate will be dropped. If the Turks won’t do the job, someone else will. Dying to make a statement may be noble, but the Turks are more pragmatic. Besides, their lives are not their own to throw away. Rufus Shinra saved them and for that they are in his debt. Their lives belong to Rufus, they must be there for him when he needs them.
How would it be for him if right after he sticks his neck out to save them they betray Shinra. It’s not like the President trusts his son. Why should he, Rufus was a traitor. Even after his release Rufus is essentially banished to Junon. The President is keeping Rufus at a distance, he gave him sparing the Turks sure, maybe to throw him a bone in the hopes he’ll stay in line. However, if the Turks betray Shinra, Rufus either looks stupid or in league with the traitors. If the President does come to suspect Rufus is in league with them, he might do digging and discover Rufus faked the deaths of the rest of the Turks and covered it up.
The President forgave one act of treason, but another betrayal, right after Rufus’s release? It would not leave the Vice President in a very good position. So the Turks must be loyal to Shinra, and carrying out the orders. Even the ones meant to test their loyalty, to punish them, the dirty work they don’t want to carry out but must resign themselves to. Not out of wickedness, or fondness for the Company, but for Rufus’s sake. He is their hope, and if they can play the loyal servants long enough for him to come to power things will get better for them, because they know Rufus Shinra is on their side. That’s the deal, he’s on their side, they’re on his, and that is why they remain loyal.
Reno says in the original game that it’s not worth it to die for your job, but what is worth dying for…when does the job matter? The instant Corneo takes Elena, it would be worth fighting, even dying to save one of their own. Rufus Shinra seems to be worth it, the Turks don’t hesitate to race to his rescue after WEAPON hits the building.
In summation, by the time plate was dropped the Turks could not refuse orders. I don’t think later canon (Before Crisis, Case of Shinra) is incompatible with original game but rather makes it more interesting by revealing another side to the story.
Bad men doing bad things isn’t nearly so fascinating as decent men, maybe even good men, doing horrible things and the circumstances that led them there.
I hope that made sense, and if any of my theories contradict canon please let me know.
Also Shademp, I don't know if you read fanfic, but I'm writing an adaptation of The Case of Shinra that goes into the events of the original games with an eye towards the characterization shown in CoS and BC. If you're interested, feel free to check it out.