Alright. Here's my theory:
In the booklet, it says that Nero's arm was injured. (This part is far-fetched, I'll admit) When he got it fixed up by whoever, it either A) was injured so badly that it needed to be amputated, and, considering how far the technology and such has gone in the Order, they were probably able to replace it, not knowing that there was a demonic power within. Or B) the injury
wasn't so bad, but bad enough for some demonic power or something to be drawn to it and squirmed its way inside. Yeah, yeah, I know- Demon possession? On just an arm? BS. Even sounds like it to me, but its just a theory.
Also, in mission 7, Nero says, "From the day forth, my arm changed, and a voice echoed, 'Power...give me more...power!' " That sounds a LOT like Vergil, doncha think? Besides, Yamato
obviously liked Nero enough to pull itself back together and help him out. The prescence of Nelo Angelo behind him in his DT helps with this, too. (It might not be Nelo Angelo, but for argument's sake, let's just assume it is.)
So, basically, Yamato is still "kept in the family" because, either way, I'm saying that Devil Bringer is a manifestation of Vergil's demonic power. -deep breath- Thanks for sitting through all that.