The snake is part of their origin story, a core element in their belief system.
Ultimately, outsiders cannot define the content or centrality of parts of a belief system. If believers say it is a metaphor, then it is a metaphor. In other words, if believers retreat empirically to the point of invisible dragons, you can't stop them. Invisible dragons aren't incoherent, they are just boring.
a large percentage of christians believe in this story,
That large sub-groups of Christians believe something empirically false does not disprove Christianity as a whole, especially since there is widespread disagreement as to who is a "true" Christian.
and two hundred years ago I'd guess almost every christian believed in it.
Citation needed. You sound overconfident here.
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Thank you for the source! (I'd upvote but have a negative score.)
If you interpret the story as plausibly as possible, then sure, the talking snake isn't that much different from a technologically superior species that created a big bang, terraformed the earth, implanted it with different animals (and placed misleading signs of an earlier race of animals and plants genetically related to the ones existing), and then created humans in a specially placed area where the trees and animals were micromanaged to suit the humans needs. All within the realm of the possible.
But, the usual story isn't that it was created by technological means, but by supernatural means. God is supposed to have created the world from some magical ability. So, to criticize the christian story is to criticize it as being magical. And if one finds it difficult to believe one part of that story, then all parts should be equally contested.
Regarding Yvain's point - I think it is true that one could just associate "stories about talking animals" with "other stories about animals that everyone knows are patently false" and then not believe in the first story as well. But, it is not just in the mind's map of the world that this connection occurs, because the second story is connected to the world. That is, when one things about Aesop's Fables you know (though not always consciously) that these stories are false.
So, to trigger the mind to establish a connection between Eden and Aesop, the mind makes the connection that "Stories that people believe are false", but the mind has good arguments to not believe in Aesop's fables, because there aren't any talking animals, and if that idea is part of knocking down Eden, then it is a fully rational way to dismiss Christianity. Definitely not thorough, and, again, it's maybe not a reliable way of convincing others.
Biologically speaking humans are animals and we talk. And since evolution resulted in one type of animal that talks couldn't it result in others, maybe even other that have since gone extinct? So there has to be an additional reason to dismiss the story other than talking animals being rationally impossible. You mention that the problem is the "magical" causation, which you see as a synonym for supernatural, whereas in Christian Theology it is closer to an antonym.
So let me tell you a story I made up:
Thahg and Zog are aliens in a faraway solar system study species of other planets. One day Thahg shows a pocket watch to Zog and says "Look, I think a human made this." Zog says, "What's a human?" "A human is a featherless biped from Earth" Zog thinks about what animals come from earth and the only one he can think of is a chicken. He laughs and says, "You think a plucked chicken made that? Boy, are you nuts!"
And of course Thahg would then look at Zog like he was nuts, because the absurdity Zog is seeing is coming from Zog's own lack of appropriate reference categories rather than an actual problem with Thahg's conjecture.
For another example suppose the Muslim woman Yvain was talking to had said "I don't believe that evolution could work because alleles that sweep through populations more often then not reduce the kolmogorov complexity of the genes' effect on phenotype." Yvain may still think she is just as wrong, but she has demonstrated intellectual engagement with the subject rather then just demonstrating she had no mental concept for genetic change over time, like the 'monkeys give birth to humans' objection demonstrates.
So the problem is saying that talking snakes are magical and therefore ridiculous sound more like "My mental concepts are too limited to comprehend your explanation" than like "I understood your explanation and it has X, Y and Z logical problems."