"Jesus, as Jew, knew the Holy Spirit as Shekinah."
No. He did not. As one who might read Hebrew He would have know "Spirit" as "ruach". As a speaker of Aramaic; much the same. As God, He knows the Spirit as something more than we can express. 
"Ruach" is still a word with a grammatical feminine gender. I'm unsure why you would have chosen something as demonstrably false as to suggest that shekinah would have been the word He may have used. In the entirety of the OT that word is not used, and only, generally, found in rabbinic (typically kabbalah) literature.
But it doesn't matter. Greek is the language for the NT and from the Greek we have "pneuma" as a neuter word, though when Paraclete and Comforter are used, these are grammatically masculine endings.  "Who", then, is a perfectly acceptable translation. I think it a silly charge to say that "fear of the feminine" (whatever that is) is a vice in the hierarchy. Seems that fear of females led men to agree to change language needlessly.