Wa alaikum assalam Ilker,
Mary is clearly referred to throughout the Quran as a female addressee. Even in the verse you cite (66:12), she is addressed as a female. Therefore one must beg the question, why is it that when we come to an isolated reference to God speaking about breathing His Spirit into ‘something’, this has questioned the whole of Mary's physiology?
Please kindly see verse 21:91 where a similar phrase is used and the singular object pronoun is in the 3rd form
female form 'fiha' in reference to Mary. It is not fantastic to note in the Quran when God fashions a child in the womb of its mother, the reference to what God breathes 'into' is in the masculine form. See verse 32:9 as an example.
With regards the claim by some that Mary could be a hermaphrodite is wholly unwarranted. In my view, such fantastic claims are borne from the inability of some to accept / reconcile Biblical portents [1] and my humble advice would be to dismiss such a claim as being totally baseless.
Regards,
Joseph
REFERENCES[1] ALLEGORICAL OR LITERAL MEANINGS TO BIBLICAL STORIES IN THE QURANhttps://www.facebook.com/joseph.a.islam/posts/362736677196799[2] THE VIRGIN BIRTH OF PROPHET JESUS (pbuh) http://quransmessage.com/articles/virgin-birth%20FM3.htm