I agree it has a lot to do with motive and morals.
For example, take DW's magic system in his "Runelords" series. I don't accept his protagonists as good, given the nature of the magic they use. In all fairness, I haven't read anymore than the first book. Neverless, the "morals", or maybe mores is the better word, of the book turned me off and I didn't want to read anymore.
In my mind you should never have to become evil, or use evil means, to fight evil. Good is a power all on it's own. And a bigger power, I might add.
In some circumstances, maybe cleaving someone's head in two is "evil means." Unfortunately, I don't have an answer for that (which doesn't help you very much, I realize). But if you need reference book, I suggest the war chapters in the Book of Mormon. I'm often surprised at the tactics that Moroni and his son Moronihah used to defend their country and their freedom.
I'm glad that you are asking these questions EUOL. I think it's very easy to get sidetracked. Look at the one woman who writes/wrote LDS romance, and started her own publishing company so that she could publish her book with pre-marital sex. Thanks for bringing this up.