The books don't count as reality in the tv show. While I think it could be interesting for a company to set movies, tv shows, video games etc all in the same continuity...in the case of Game of Thrones, the book did not "happen." So, when judging a character, you have to go with the tv show continuity...although it would be wrong to drastically alter the character from the source (it would be wrong to have a Jason Voorhees tv show where he is a hunky teen who dates a bunch of hotties, for instance).
I know that audiences have accepted all kinds of awful behavior from characters that turn good. Personally, I'm not sure that I could ever cheer for a character that knowingly attempting genocide in an effort to overthrow and enslave the world. I'm really not sure what it would take to make me accept that person as a hero. I've always been a bit of a stickler with characters maintaining their cores while evolving in more natural ways.