All perfect praise be to Allah, the Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and Messenger.
What you mentioned, that the addressed person is an atheist and her name is indicative of Shirk, does not affect the permissibility of talking to her and calling her with her name. This is not considered assertion of Shirk; it is merely an assertion of the name she is known by, and this is permissible.
Ibn Al-Qayyim wrote, "The statement of the Prophet, sallallaahu ‘alayhi wa sallam, 'I am the son of ʻAbd Al-Muttalib,' was not intended to approve the use of this name; rather, he was simply mentioning the name by which that person (his grandfather) was known. Informing people of a name to identify the person spoken about is not prohibited. The issue of informing is of a broader scope than the issue of giving a name." [Tuhfat Al-Wadood]
Allah knows best.