If I understand what you're saying, I think you're referring to the ability to kill whomever you please, perhaps with the exception of major plot-moving characters.
A couple of things wrong with this:
1. Anytime you give a player the ability to indiscriminately murder whomever they please within a game, including civilians, it automatically gives the game grounds for an M rating. Zelda should never be an M rated game.
2. As much as one would like to believe that people don't copy what they do on video games or see on TV, unfortunately they do. Why do you think there's been such a controversy over the Grand Theft Auto series? Because people do copy those things. For every intelligent, independent person in the world, there are several stupid people who still operate on the "monkey see, monkey do" principle.
3. Think about other games that implement such a high degree of freedom in the games, like GTA, Elder Scrolls, Fable, etc. They have to introduce a form of a moral justice system. For example, if you kill someone or steal something, you go to jail or you get attacked by guards, police, etc. This is more of a freeform game idea where you can become who you want to be and do what you want to do with your created character. Link is not a character you create. He is irrevocably the hero. Does indiscriminate murder seem like something a hero would do?
4. This does not apply to Ganondorf or his cronies because he is established as the root of evil in the game. Think about it this way. In a game which children can potentially play, do you really want gray area as to who is the hero, who are the innocent, and who are the ones who are explicitly evil?
I understand the desire for increased freedom in a game, but Zelda isn't a freelancer kind of game where you can do whatever you fancy.
There are some very good freelancer games out there that I would encourage playing, like Fable, Elder Scrolls, etc. in which you can actually do that sort of thing, but don't expect it in Zelda.
