The Gemara is clear. He is simply explaining it.
If you found a certain Baal Tosfos, fine. But to put this on Rashi is a terrible accusation, pinning on our greatest Rishonim what the Zohar Hakadosh says is part of Arur Asher Yaase Pesel Umaseicha Vesam Basseser, is horrible. These references were glossed over for a thousand years and nobody thought of it what the recent researchers found with their newly found zest for all things odd.
It is actually pretty ridiculous to claim something like this when our Neshama is not Megusham and does not have a form. The Gemara says that Hakadosh Baruch Hu fills the world like a Neshama fills the body. Was Rashi ignoring this when he translated Bitzalmeinu the way we all do today?
Does the Gemara in Brachos 6 also show this Shita when Rebbe Yishmael mentions nodding of the head? Does the Gemara later discussin clapping hands, kicking feet, sighing and crying also promote this ‘shita’? Why does Rashi go at such lengths to explain Vayisatzev El Libo? Why does he find it necessary to explain Erda Na?
Just because Rashi didn’t make a More Nevuchim to explain how such terms come in, that doesn’t mean that he didn’t have any deeper understanding of such matters. As the Yashar Micandia writes, if I were to write you a math book does that show you that I don’t know philosophy?
It is also hard to gleen what someone held from a critique against him. The Rambam complained about a Sefer Shiur Koma. Presently, we don’t give such a thing a second thought.