So, if Alphonse Elric is such a brilliant alchemist, how could he be duped into misinterpreting his own blood seal and being scared that his brother just created him (and believing the words of a sketchy criminal hanging around some abdandoned lab)??
Well, I just recently did the same thing. If you want to know the full meaning of the components of Al's blood seal, here's what I've found:
I came across this little tidbit on DA the other day: Basic Alchemy Symbols by Notshurly. That one symbol there on the left (creation) looks astonishingly similar to something we FMA fans are so familiar with: Al's blood seal . (I don't know how much credibility you give to DA alchemists, though, so just in case, here's another source reinforcing the same thing.) Well, if that little squiggle there represents the soul (which would be your first assumption, right?), then holy crap! That sounds like it would mean that seal is the creation of a soul, exactly what Alphonse was afraid of, right? So I went scouring the internet looking for proof that that little squiggle is the symbol for the soul. The closest thing I found was this right here. Look at that third one over from silver. Considering I found nothing else even close to resembling that squiggle any more than that symbol for silver right there, I looked up some alchemical meanings of silver. One meaning I found was bascially, that silver=moon=spirit, and I though "Wahla, there it is." But in actuality, the spirit is not the same thing as the soul.
Many philosophers (Descartes is coming to mind right now, but if I'm not mistaken, there were a bunch of others around this time) believed that there was a material in the human body which connected the soul to the body, and this material was sometimes called the spirit. So the array that Edward drew with his blood is literally the creation of the bond between a body and a soul.
Unfortunately, that didn't turn out to be the dark theory I'd hoped it'd be, but hopefully you learned something from this like I did.
At the least, you can see that Al's fear wasn't completely unfounded. He wasn't just being a gullible little kid believing the words of random criminals. The meaning of the blood seal was easily misinterpreted.