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There's a statement attributed to the Vilna Gaon (quoted in the introduction to Binas Mikra and in several other places) that the Mishnah can be interpreted according to 'peshat' which can sometimes differ from the Gemara's understanding of those Mishnayos, just as pesukim can have a 'peshat' which doesn't conform to halacha.
Are there other sources (besides for those quoting the Vilna Gaon) for such an idea, or anyone who explicitly refutes this position?
Yes. Tosfos Yom Tov (Nazir 5:5) writes that just as earlier commentators were willing to explain the Torah according to a peshat that doesn't conform with the Halakha, we may do the same when it comes to the Mishnah (as long as we don't present it as being the halakha). More on this methodology is discussed by R. Kalman Kahane in Heker VeYiyun I, pg. 150-152
Additionally, there are also sources (Gra-related and otherwise) on a similar topic: The Netziv (Sheiltos Bamidbar 128) says דרך הגמרא לעקם פירוש המשנה כדי לאוקמה הלכה, the Gemara will distort the intended meaning of the Mishnaic text in order to have it conform to the Halakha. Such a position was likely influenced by writings of the Vilna Gaon's students, as this is explicitly stated in his name by his student, R. Baruch of Shklov, in his introduction to the Pe'as Hashulchan.
There are a few earlier sources for such an understanding, to give a few examples (out of many):
Ramban to Gitin 82a says that a particular position is that of the Amoraim alone who are 'hanging' it upon the mishnah
Rif (Brachos, Rif 24a) writes that he'd rather pasken the halakha according to the mishnah's simple reading than according to forced explanations in order to fit it with other opinions
The Meiri in his introduction to Maseches Avos refers to these odds methods of 'interpreting' Mishna as לחלוק עמהם בקצת דברים, and R. Havlin's footnote there connects his position to that of the Netziv
Almost all acharonim, particularly chassidim make this. The Toldot Yaakov Yossef quoted several times a mishna in kidushin concerning Yichud. Erllier, Maharal interpreted in psacim זיתום המצרי ושכר המדי וחומץ האדומי...as an allusion to Galuyot.
An entire book on Mishnayot called Maasse Rokeach is only drushim al pi Kabbalah on mishna.
The introduction of the book addressed the link between Mishna and pardes.
The Baal Hatanya most certainly does. On the Mishnah in shabbos that all animals that go out with collars... He explains it to be talking about angels and their song.
