Are you 

>! Ali 
>! <br>
>! <br>
>!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 
>! <br>
>!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