Are you
Ali
The cousin and the son-in-law of Muhammad, the last prophet of Islam.
I was born in a holy place, holy for a separate reason.
Mecca
Mecca is considered the holiest city in Islam, as it is home to the Ka‘bah
I was met with a great man's face, a sight that's been lost through the seasons.
Ali saw Allah, it is now forbidden to portray him.
I was killed in an empire's base, victim to a violence and treason.
On 19 Ramadan AH 40, which would correspond to 27 January 661, while praying in the Great Mosque of Kufa, Ali was attacked by the Kharijite Abd-al-Rahman ibn Muljam.
Hint 1:
Ali Khamenei, Ali baba, Muhammad Ali.
Hint 3:
Ali G