I'm not sure if I'd watch it, but I honestly don't know a whole lot about it. As others have stated, pray and follow your convictions. If God doesn't want you to watch it, you'll know.
From my own personal experiences, I've found titles that fellow Christians enjoy that I personally avoid. D.Gray-man, Hellsing, and Kamikaze Kaitou Jeanne are anime series that I've looked into, but avoid because I felt the religious content in them was too off for me. The Melancholy of Haruhi Suzumiya is another one that I don't particularly care for, because I don't really like the fact that they say Haruhi is God. But - as stated before - I do know others who enjoy these shows. While I feel differently about them, I respect the opinions of others. I know that I feel convicted about things differently than they do, and I'm not going to force anybody to follow my convictions.
I also used to be a lot stricter with my content than I am now. When I first started watching anime, I wasn't into most "magic" as a whole, but as I started to learn more about the culture, I grew used to most things and could accept more than I could before.
I'm a fan of FMA and Bleach, but I can understand those who avoid those titles because of how spirituality is portrayed. I *personally* view the spirituality in these shows as fantasy, and not necessarily anything I would take literally. If one were to take it literally, I would recommend avoiding the shows.
As far as Vampire Knight goes, I'm a huge fan. I don't see why somebody would be convicted about spirituality (unless they dislike the vampire genre as a whole), but I can think of another reason why a person would be convicted... (In Vampire Knight Guilty) [spoiler]...In regards to the hints of incest.[/spoiler] But regardless of whether or not one feels they should avoid it for this reason or because of spirituality, people are free to watch what they want and not watch what they don't want. I know other people who don't care for it, and I respect that they dislike it. They're free to hate anything as much as I am to love it (and vice versa).
So, in regards to this particular series, I say that you can watch it if you feel like God isn't telling you otherwise. Pray, possibly watch a few episodes, and go by what you're thinking God is telling you.
God bless!