I wrote a big thing and deleted it 'cause all I really had to say was that I think you're worrying about nothing. You can't control how the audience reacts to your work and if you're really so afraid of the audience misinterpreting any kind of ambiguity, don't include any ambiguity. If you want to make it clear that your character's morality is wrong and misguided, make it clear through a separate character, since you've eliminated a third person narrator. Make sure that this character following his immoral path is punished in some way.
My personal two cents, anybody who extrapolates much of anything about a creator from his work (especially a single work) is a fool. A writer is just as likely to write about what he dislikes as what he likes. Some writers write about how they see the world, others how they think it should be, while others write about how it could be, never was, never could be, never would be, never will be.
For instance, Mercedes Lackey really likes to have sexual deviants as her villains. Does that mean she doesn't like sexual deviants and thinks of it as a necessarily villainous thing? Or is she a sexual deviant who realized that by having her villains be sexual deviants, she could write about sexual deviancy with no one being the wiser that it was her biggest turn on?
Avoid internet douchebaggery. Never post on forums.
Crazy Kiwi
Personally, I like to think that William Gibson doesn't want the world to be a dark technodystopia with all the "good guys" being drug-addled antiheroes, so tend not to make assumptions about the writer based on the content of the stories.
I make an exception in the cases of the Brothers Grimm - I think they were seriously screwed up 
I don't think you have anything to worry about. Nobody watches The Godfather and thinks that the director thinks being a gangster is an acceptable career choice.
edited 4th Dec '14 7:29:08 PM by AmbarSonofDeshar
<chirps obnoxiousy>
Just a follow-up question: what do you think about writing something where the characters agree with something that you think is wrong but you think tons of people might agree is okay? For example (it's a lame one, but bear with me), let's say the author believed that religion was totally heinous because it gives people false hope. Yet there are tons of people in the world who believe that religion is a good force (provided it doesn't hurt others). The author, let's say, writes a hero whose religious background plays an important part (because it gives him a superpower or something, let's say).
If the author didn't want to give the message that religion is a good thing but knew that a lot of people would agree with this message, wouldn't that make an impact on the way the author's work is interpreted? I don't know, it's overthinking but society does have a way of making certain aspects of a work more relevant/popular (e.g. in the form of an Accidental Aesop).
Write your story first, and worry about the morality of it later. If you write honestly and sincerely, then your beliefs and values will shine through anyway.
edited 10th Dec '14 1:12:05 PM by Tungsten74
I am planning a new story: not writing, as I'm currently focusing on something else, but I'm at least in the beginning stages of idea-gathering. The idea, I think, is a pretty solid one, and I would be invested in writing this story (granted, once I'm finished with the one I'm currently working on). However, it's a genre that I've never really tried before. The lead characters in the story have strong moral principles, but they also do things for them that are morally unscrupulous and that I personally don't believe are right.
Characters will do things that authors don't agree with—that's a fact. My main conflict, though, is dealing with a sort of "writer's dissonance." My current story has much "nicer" leads, in that they are for the most part moral—and if they do anything immoral they immediately feel remorse. For that story, I really want to stress the importance of the characters' beliefs and actions.
What I'm afraid of with this new idea is that my readers are going to assume that I am completely on-board with the things that these characters do when I'm not. I know how to emphasize certain ideals that the characters and I share, but the characters don't think that certain things that they do are immoral, so they are not going to admit they are immoral (it's first-person perspective). I'm worried that readers might not get that, given that my past works had "stronger" moral paths to follow.
So, is there any way to solve this dilemma? Or maybe I'm putting too little faith in the reader's ability to distinguish moral issues? I personally think that regardless of what kind of character you write, you should embrace the good they do, but in this situation it's difficult for me to think about how my readers will perceive these new characters and what they may take from them.
And, additionally, I wonder how readers will perceive my own values. I think it's interesting that we assume certain things about a writer based on his/her subject matter. Is there a way for a writer to distinguish himself/herself from characters? Or are they ultimately linked together, and the writer is the only one who can speak for his/her own views? Just some thoughts.