To understand the question I have read chapter 7 from http://www.judaismvschristianity.com/ and here is my impression of the argument as someone who has spent thirty years studying the scriptures, church history and doctrine.
First, the article is not remotely scholarly nor is their any scholarly debate to support it. Outside of a few confused interpretations of a few biblical events, it does not cite any external history or facts to support the argument. For this reason there is no 'scholarly refutation' of the argument, since the argument is not recognized academically. Therefore, my response may be the closest thing to scholarly as I am at least willing to investigate the claim and provide a reasoned response to it, whereas most scholars would not be bothered.
Second the article uses information that naturally oppose the argument itself making it not only not scholarly but completely illogical.
As the argumentation is so flimsy and unsupported by scripture and church history I will only outline the authors primary argument and show how easily it can be dismissed as sham logic.
It is argued that his Apostleship was unrecognized by the other Apostles.
Answer: Anyone familiar with scripture would realize that he was fully recognized by all the Apostles, otherwise the letters of the other Apostles would have warned congregations of this 'false Apostle'. Instead they gave him full support. For example, Peter knowing Paul often referred to himself as 'an Apostle' in his letters (because there were false teachers who challenged his Apostleship) said this:
Bear in mind that our Lord’s patience means salvation, just as our dear brother Paul also wrote you with the wisdom that God gave him. He writes the same way in all his letters, speaking in them of these matters. His letters contain some things that are hard to understand, which ignorant and unstable people distort, as they do the other Scriptures, to their own destruction.
Therefore, dear friends, since you have been forewarned, be on your guard so that you may not be carried away by the error of the lawless and fall from your secure position. (NIV 2 Peter 3:15-17)
Here Peter infers Paul's letters are also the scriptures which unstable people distort. That means when Paul said he was an Apostle, Peter included the statement as scripture.
This verse also, so succinctly describes the argument of this author in his article on the website. Everything argued in so contrary to serious thought and expresses such ignorance of the scripture that it must come from an 'unstable mind'. Even a stable minded unbeliever would recognize that if Paul had hijacked Christianity history would have recorded great conflict between Peter and Paul, yet no such conflict is recorded in Christian history. Furthermore, a stable mind that does believe in Christ would find it highly improbable that the Messiah would have established a new kingdom and glorious phase of Salvation history upon a Rock (which the gates of hell could not prevail against) and then immediately allow a false Apostle, quickly overthrowing that kingdom. (Ref Math 16:18)
The rest of his arguments are similar and as easy to shred into pieces, but since the foundation of his theories are already laid waste their is no apparent purpose to proceed.