First, the OP phrased its question: "What Rabbinic interpretations of the Garden of Eden narrative treat "the serpent" as more the protagonist, instead of the antagonist?"
The OP's choice of words seems to say that the questioner has already made the conclusion that there must be certain interpretations; and we just need to ask who out there knows of them?
A Torah scholar seeking truth should rather phrase it:
Are there any interpretations of the garden etc..."?
We should ask in a way that the question shows we are willing to accept the possible fact that no Rabbis ever interpreted the story in that particular way at all.
Second, if someone wishes to answer that there are no such interpretations by the Rabbis about Adam Eve and the Snake, The OP could then say: Prove It !, And no one could prove it unless they can claim photographic memory of everything every Rabbi ever said and claim the OP's interpretation is not in there.
So I will respond by saying that I have attended Orthodox Jewish religious schools since I was a boy and have learned quite a lot on that chapter in Bereshis. I am a Rabbi and I am 48 years old. I have not been able to recall having ever seen or heard anything the OP is looking for about the Snake being the protagonist etc.
In fact, it smacks of a completely non-Torah concept which might be applied to scholarship concerning Greek Mythology, but not the Torah of Israel.
The Torah teaches moral lessons and when those are taught in a "story" form, it is consistent in that the characters of those stories if portrayed as good, are good... and if evil are evil. They do not switch around roles.
What they could do is be made to show that the good guy is sometimes challenged by evil and the bad guy also has measures of goodness about him. IOW, sometimes characters in the Tanach are 3 dimensional and have aspects to their person that is not always 100% black and white.
However, this does not mean that a protagonist will flip and become the antagonist etc.
Cain killed his brother Abel. Cain is the antagonist because he is in fact a foul murderer and Abel is an innocent victim or the protagonist. Thats all. No switching or secret teachings or symbolisms etc.
However, there is an opinion among the Rabbinic works (Medrash) which explains that Abel was subject to Cain's attack because Abel needlessly caused his brother to be jealous of him.
But even according to this "interpretation", Cain is still a murderer, and still wrong, 100%. The Medrash is simply trying to present a reason why Abel might not have merited protection. Even so, he is still the righteous victim in the story. That cannot change.
This type of question from the OP, is actually dangerous as well.
Certain outcast groups in Jewish history thought along these lines. for instance, the Frankists (offshoot followers of Shabatai Tzvi the false Messiah active in the late 16 - 1700's etc.), held a belief that since G-d loves repentance, it is actually a good idea to sin terribly so that you can repent and please G-d.
Of course that is total insanity, but it is an example of what happens when someone "flips" tenets of Judaism just to experiment with mysticism. It is dangerous nonesense.
Torah and Judaism are not novels open to free interpretation. No one should approach it as if every opinion is valid and respected. Its not so. Only real Torah scholars with real sources may make comment and teach Torah thought. This is especially true when someone raises the banner of "Kabbalah" etc.
Judaism and Torah thought are made to be based upon real tradition and well defined attitudes, so Jews can follow the truth without doubt and without thinking that every whim is another truth.
It may sound boring but it has integrity. If we were to allow the OP its fullest conclusion, then anyone could identify with Esau or Laban or Pharoah or other evil characters in the Torah, and make them somehow the protagonist. Eventually, that person would not know right from wrong and justify their evil choices in life by saying that they follow some flipped interpretation of a Torah story.
That would be a disaster. Lets keep things straight and simple... and True. :)