There is a refutation of Hislop's work in print. It is called "The Babylon Connection?" by Ralph Woodrow. I own it. It could be more indepth.
Ralph Woodrow was a proponent of Hislop's and wrote a book using Hislop as a main source. Once he realized he was incorrect, he pulled his book of the market and wrote a refutation.
Here is the Amazon write up excerpt from the book:
"In my earlier Christian experience, certain literature fell into my hands which claimed paganism had been mixed into Christianity. While the Roman Catholic Church was usually the target, it seemed other churches had also been contaminated by customs and beliefs for which pagan parallels could be found.
"The Two Babylons" by Alexander Hislop (1807-1862), with its alarming subtitle, "the papal worship proved to be the worship of Nimrod and his wife," was THE textbook on which much of this teaching was based. Over the years, this book has impacted the thinking of many people-ranging all the way from those in radical cults to very dedicated Christians who hunger for a move of God and are concerned about anything that might hinder that flow. Its basic premise is that the pagan religion of ancient Babylon has continued to our day, in disguise, as the Roman Catholic Church and is described in the book of Revelation as "Mystery Babylon the Great"-thus, the idea of TWO Babylons, one ancient, and on modern. Because Hislop's book is very detailed, having a multitude of notes and references, I assumed, as did many others, it was factual. We quoted "Hislop" as an authority on paganism, jut like "Webster" might be quoted on word definitions.
As a young evangelist I began to share a sermon on the mixture of paganism into Christianity, and eventually wrote a book based on Hislop-"Babylon Mystery Religion." In time, my book became quite popular, went through many printings, and was translated into Korean, German, Spanish, Portuguese, and several other languages. I came to be regarded by some as an authority on the subject of pagan mixture. Even a noted Roman Catholic writer, Karl Keating, said: "Its best-known proponent is Ralph Woodrow, author of 'Babylon Mystery Religion'."
Many preferred my book over "The Two Babylons" because it was easier to read and follow. Sometimes the two books were confused with each other. Letters in a steady flow were received praising my book. Only occasionally would there be a dissenting voice. ONE WHO DISAGREED was Scott Klemm, a high school history teacher in southern California. Being a Christian, and appreciating other things I had written, he began to show me EVIDENCE THAT HISLOP WAS NOT A RELIABLE HISTORIAN. As a result, I realized that I needed to go back through Hislop's work, my basic source, and prayerfully check it out!
As I did this, it became clear-Hislop's "history" was often only mythology. Even though myths may sometimes reflect events that actually happened, an arbitrary piecing together of ancient myths can not provide a sound basis for history. Take enough tribes, enough tales, enough time, jump from one time to another, from one country to another, pick and choose similarities-why anything could be "proved"!
The concern about not having anything pagan in our lives can be likened to a ship crossing a vast ocean. This concern has taken us in the right direction, but as we come to a better understanding as to what is actually pagan and what is not, a correction of the course is necessary in our journey. This is not a going back, but a correction of the course as we follow "the shining light, that shines more and more unto the perfect day" (Prov. 4:18).
Although we challenge some of Hislop's claims in THE BABYLON CONNECTION?-this is not intended as an attack against him personally. As far as we know, he was a dedicated Christian, a brother in Christ. Nor is it our goal in writing this book to merely discredit another book. Instead, it is our desire that this effort will help us understand "the way of God more perfectly" (cf. Acts 18:26), find a biblical balance, and glorify Him who said: "I am the way, the truth, and the life: no man cometh unto the Father, but by me" (John 14:6)."
I've found that most of Hislop's claims can be discredited just by using the internet and the vast amount of historical informaiton and writings that are available. In years past trying to get some excerpt from a book from antiquity would be a daunting task for the most ardent seacher. Now, with the internet, it's usually just a few clicks away.