My protagonist is Eris and my antagonist is Ezrith.
In a post-apocalyptic world, my unreliable narrator Eris has the ability to control and manipulate life and subsequently kill any living thing at will. She denies her abilities because of an extremely traumatizing event in her childhood, where she murdered her aunt, father, and sister accidentally, and while trying to cover it up, killed more people who came to investigate. She has been found by a group of survivors and taken a liking to the adopted son, Caspian, of the group's matriarch, Ezrith.
Ezrith is the antagonist. Her dead wife Saskia, Caspian's biological mother, was killed while on a scouting mission (unbeknownst to Ezrith or anyone in the group) by Eris, who has blocked out the memory of the murder. Ezrith is extremely suspicious of Eris and constantly scrutinizes Eris' motivations and behavior.
The fact is, though, that Ezrith's motivations (despite being Eris' antagonist) are totally benevolent and her love for her son and the group she leads is pure. All she wants is to keep her loved ones safe. Eris, on the other hand, is selfish, secretive, and bottom-line morally compromised, killing out of fear and hatred and lying to herself and others.
Is this plot line even feasible? Can I have an effective portrayal of an "evil" protagonist and "good" antagonist without having my reader sympathize with the antagonist? And how can I keep my reader's sympathies aligned with my protagonist despite all of her somewhat unredeemable faults?