Manga safe for kids?

I have a pre-teen daughter whose friend reads a lot of manga and watches a lot of anime. Recently my daughter started watching Full Metal Alchemist.

My wife and I have watched some of FMA and are little disturbed. The violence is pretty graphic with characters walking through puddles of blood. Also, the drawings are quite dark and I found themes like a corrupt ruling military potentially too mature for an eleven year old. That said, my daughter is fairly sophisticated for her age so we might have been willing to overlook these.

The element of FMA that has really got us wondering is the focus on death and souls - more specifically the ways in which souls are manipulated, bodies stolen, soulless creatures created and souls harvested to create a philosophers stone. My wife and I are struggling with the unwholesome nature of this series and do not think that the occult theme is balanced adequately by redemptive elements.

The question that I hope someone in Blogland can help me with is this:
Are we overreacting or should we not allow our children to watch this show until they are older?

On a related note, when he was seven, we stopped my son from watching the Yu-Gi-Oh cartoon whose plot including soul-stealing. Is this a common theme with manga and anime and something to which we as parents need to pay special attention?