I definitely agree with the article and have said so myself many times. I can't say for sure that it advances replacement theory, but it definitely helps ease one into such an idea.
For the most part though, I suspect it has more to do with the fact that most Christians don't really realize how dissimilar Judaism actually is from Christianity. My experience has been that they have difficulty swallowing that it is halachically easier to walk into a mosque than a church. They just assume since Christianity has Jewish roots, it must share core beliefs.
In my journey from Christianity to Judaism, and the myriad of discussions I've had by those Christians trying to win me back, I have really come to see this very clearly, and I can understand why it is the case. For the average professing Christian who was raised in the Christian faith the only way to look at the Bible is through a Christianized lens. It's not until one is able to make the "suppose I read this as if I weren't already a Christian" leap that it all becomes clear.
Ultimately that's what did it for me. I took a step back and said, "If I read this as if I have no opinion on it, Jewish or Christian, what conclusions can I make?" and the rational outcome was that it's impossible to see Christianity as anything other than a poor perversion of Jewish scriptures in pursuit of a worldview that preys on the weak and emotionally needy.
As much as I dislike speaking badly about other religions, the more that I deal with the stark differences between Judaism and Christianity, the more I feel that the religion itself is a terrible thing.
Granted, I don't blame the people for what most of them have no real control over having been raised with a paradigm that discourages honest criticism, but I see it pouring into every aspect of American society. God forbid they learn you're Jewish, because then it becomes this pathetic attempt to bring you to the "true Jewish religion" (a problem I'm currently dealing with in an acquaintance of mine).