In my opinion it all depends on the context you write in.
If my "hero" spends his time wantonly murdering and killing people, one whose favorite pastime is raping and pillaging, then yes I am glorifying evil actions (the so called "anti-hero" popular in some circles). But, if my hero is striving against such a foe and he (or she) consistently chooses to do the right thing, however hard, then I'm not glorifying evil actions. Instead I'm illustrating the human condition. We all must daily struggle against sin. That is the nature of Free Will. I believe that it's important also to show that the protagonist has to struggle with his/her choices - because we all do. If you hero never wavers, never has to struggle with choices, then he/she becomes less relatable to the reader.
That's a barrier to allowing your reader to identify with your protagonist. Personally, I want my reader to become invested in my protagonists, after all I'm invested! I want to share their triumphs and their sorrows. I want my readers to care.