Agreed, giving Vergil a gun basically butchers his entire character. He didn't dislike guns because of a code, he disliked guns because he thought they were cheap. To him, using guns was the equivalent of picking Naruto in MUGEN. No matter what Naruto you pick, it is always going to be cheap as hell. He found using guns to be a dishonorable technique of picking on your opponent.
1. actual samurai had nothing against guns and used them as soon as they were available. Vergil's dislike of guns is not a samurai trait it is Vergil's own personal preference (and it is not really a code he was perfectly comfortable using one of Dante's guns he just prefers not to).
I think he just used guns here because he decided to "Try it Dante's way for once." I guess I'm getting this code of not using guns from that movie "The Last Samurai" Where they refused to use guns.
2. DmC is supposed to have more western themes so there would be no reason for them to make Vergil follow an overly idealized 90% fictional version of Bushido. Unless they plan on turning Vergil into the type of hero that refuses to kill anyone there is no reason to not give DmC Vergil a gun other than the fact that DMC Vergil prefers swords.