SOLVED. Female assassin who is potentially the reincarnation of Christ commits murder and is condemned to death, and she has distinctive green and blue eyes. [s]

[Zachary]

I read this book in high school. I think it's about 300 or so pages in length, this girl is trained from a young age to serve an agency to kill high ranking people. She has one blue eye and one green eye, she's conflicted about what she does, and the truth about her origins are kept from her, but a detective character sort of figures it out. She commits a kind of murder on a priest or somebody and she is caught, she is then condemned to death, I think in prison. That's about all I remember of the book.

[Avaminn]

Could it be Graceling by Kristin Cashore? Only parts of your description fit but it involves a female assassin with one blue and one green eye.

[Sophie]

Could it beGrave Mercy by Robin LaFevers

[Zachary]

I found it! It's the miracle strain by Michael Cordy. I thought it was pretty influential in high school. Time to see if it stands the test of time.

[Kris]

Glad you found your book, Zachary. Here's the link - The Miracle Strain by Michael Cordy.