Thank you, Aussie, I now have a computer, and you reminded me that I was supposed to post in here 

Now, first of all, I think that this can be done, but it has to be done the right way so that there is no question what is right and what is wrong.  I don’t think we should portray something wrong as being right.  However I do think your character can do something “wrong”, and be right in doing it.  Did I confuse you?  I have a tendency to do that, but I will hopefully explain it all so that you are no longer confused.  Now, let us begin.
Okay, how many of you have seen the movie National Treasure?  If you haven’t, go watch it!  I absolutely love this movie.  It is one of my all time favorites.  
Now, why do I bring this movie up?  Because this movie has the perfect example of what we are discussing.  In the movie NT, Ben (main character) views himself as a treasure protector.  We love Ben Gates.  Why?  Because Ben worships history and has led a life that was dedicated to protecting the history of America.  The founding fathers are his idols.  He looks to their standards to help shape his life.  And he is search for a treasure, one of great historical and intrinsic value.  What is the problem?  He finds out, through a series of clues, that the invisible map is on the back of the Declaration of independence.  

  That’s right people, one of the most important and heavily guarded documents in our nation.  Now here is the problem.  Ian, the bad guy, says for Ben to let him deal with this.  He will… how did Ian word it?... anyways, Ian is gonna steal it for them.  Now, Ben, being the wonderful character that he is, says “no, Ian, I’m not going to let you steal the declaration of independence.”  A gun fight and lots of action and explosions ensue, yadayadayada, I won’t make you all sit through my ranting on how  wonderful this movie is 

Now what happens next is interesting.  This is what Ben says to the delightfully lovable Riley:
Ben Gates:  Of all the ideas that became the United States, there's a line here that's at the heart of all the others. (reads the Declaration of Independence) "But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute despotism, it is their right, it is their duty, to throw off such government, and provide new guards for their future security."  People don’t talk that way anymore.  
Riley Poole:  that’s beautiful… And I have no idea what you just said.
Ben:  It means if there's something wrong, those who have the ability to take action have the responsibility to take action.  (continues to stare at the Declaration) I’m going to steal it.  
Riley:  (chuckles like it is a joke, looks at Ben, sees he’s not joking and his eyes get big).  What?
Ben:  I’m going to steal the Declaration of Independence.
Riley:  (nervous disbelieving chuckles as Ben walks away from the display).  Uh, Ben-
NEXT SCENE
Riley:  This is... huge.  Prison… huge. You are gonna go to prison. You know that, right?
Ben Gates:  Yeah, probably.
Riley:  Well... that would... bother most people.
Ben:  Ian is going to try to steal it, and if he succeeds, he’s going to destroy it.  The fact is that the only way for me to protect the Declaration of Independence, is for me to steal it.  It’s upside down.  I don’t think there is another choice.
Riley:  Ben, for goodness sakes, It’s like stealing a national monument.  It can’t be done.  Not just that it shouldn’t be done, it can’t be done.
From here the story goes on.  But the line I really want to hit in on is this one.  Ben says this to Abigail (who doesn’t know his plans) right before he steals the Declaration.  He cryptically says this to her, in a toast:
Ben: A toast.  To high treason. That's what these men were committing when they signed the Declaration. Had we lost the war, they would have been hanged, beheaded, drawn and quartered, and-Oh! Oh, my personal favorite- had their entrails cut out and burned!  So... Here's to the men who did what was considered wrong, in order to do what they knew was right...  what they knew was right.
And that statement is so true.  There are times in our lives and histories when we do have to do what is considered wrong.  Our founding Fathers did.  But they did it because it was right!  Jews were hidden from the Nazis because they knew it was right!  I think that we can deal with these subjects, but there is a right way to do it.  Make sure that what your character is doing is right.  They may break laws and commit crimes to do it, but it is the right thing to do.  I am a firm believer that breaking the law when something is right, is the right thing to do.  And I will do it, if our world comes to that point before I die.  
However, I don’t think we should allow our characters to do wrong for something that is not necessarily right.  It needs to be right.  I don’t think it is beneficial for us to mix messages and blur the clear lines of scripture.