Basically, I used to be an agnostic and am not any longer partly because of the shoddy historical assumptions among the skeptics and debunkers, particularly when compared with the primary sources. Too often, there is an assumption almost that *because* it is an old tradition, it *can't* be true--no matter what history says to the contrary.
It is true that James was certainly the head of the Church of Jerusalem...and that a sort of nucleus of Jewish Christians had grown around that see until the city was razed by the Romans and the Jews expelled--around 160ish I think it was. I know of, however, no early source that would exactly support the author's theory of "two Christianities", and in particular one which would oppose the headship of James in Jerusalem to that of Peter in Rome. Certainly Irenaeus, writing around 160-170, ascribed to Peter a role which he does not ascribe to James. Perhaps your author is thinking of the Quartodeciman and similar controversies.
Anyhow, here's Eusebius's account of the martyrdom of James:
http://www.newadvent.org/fathers/250102.htm.
Scroll down to chapter 23...the excerpt is too long to include here, but basically Eusebius, writing in the early 300s, has a long quotation from Hegesippus, a writer in the second century, narrating James' martyrdom because he confessed that Jesus was the Christ.
I will do some homework in the primary sources though on the relation of Peter to James and see what I can find.
since you are interested in early church history and archeology that proves it up, you really must read the book.
In addition to the central thesis, (eg, that the dynastic family relations of Jesus and John the Babtist made them logical and palatable purveyors of the messianic movement in a time of Jewish ferment), it has some fascinating scholarship and information about locations of burial chambers and burial ossuaries found there.
Most folks don't even realize that Jesus had a number of brothers because the New Testament books sort of gloss over them and the names are so common that the references are mixed up.
Likewise some interesting stuff on the relationship between Mary and Joseph.
I couldn't put it down.