Does the pronoun in "and whoever intends [to commit] therein any wrongdoing" refer to Mecca, or the Sacred Mosque, or the resident within the boundaries of the Haram, and what is the meaning of "إلحاد" (deviation/wrongdoing)? Does it include minor sins, or major sins, or what the self whispers but has not yet occurred?

The pronoun (فيه - in it) in the noble verse refers to the Sacred Mosque, and according to the most preponderant scholarly opinions, it encompasses the entire Makkan Sanctuary, as indicated by other verses, such as His saying, the Exalted: "That is for he whose family is not in attendance at the Sacred Mosque," and His saying: "Exalted is He who took His Servant by night from the Sacred Mosque."

Atheism (Al-Ilhad) in the Arabic language means inclination, and what is meant by it here is inclining towards disobedience to Allah and violating His law, meaning legal transgressions in general. As for mere self-whisperings or what crosses one's mind without speaking or acting, one is not held accountable for it. However, the firm intention to commit a sin is held accountable, and it becomes more severe within the Sanctuary.