What's the song when Shiro is dying in the main chapel?
It's "Banner-Seal of Heterodoxy: The Son of Deus", the 4th track from "Ninja Resurrection (Original Soundtrack)". The preview of the OST can be listened on AllMusic.

According to the OP's comment,


  it's the 4th song from the link you mentioned! Banner-Seal of Heterodoxy: The Son of Deus.