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.

>! The second period of Ali's life began in 610 when he declared Islam at the age of 9, and ended with the Hijra of Muhammad to Medina in 622. When Muhammad reported that he had received a divine revelation, Ali, then only about nine years old, believed him and professed to Islam. Ali became the first male to embrace Islam.Shia doctrine asserts that in keeping with Ali's divine mission, he accepted Islam before he took part in any pre-Islamic Meccan traditional religion rites, regarded by Muslims as polytheistic (see shirk) or paganistic. Hence the Shia say of Ali that his face is honoured, as it was never sullied by prostrations before idols.

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