Perhaps something similar to Spec Ops: The line?There is no morality system as such but you are given moral choices with no choice being truly right or wrong.
While I've never played Spec Ops: The Line, I believe that a mix of what your are suggesting and some Fable reputation system may fit Destiny best. Personally, I want it all completely invisible to the player. This way there are no preconceived notions about what is right or wrong in this game.
I'm currently playing through Mass Effect 3, and there was a conversation where I was prompted to do the Renegade action if I so chose. I remembered that most of the time in Mass Effect 2, that conversations would either prompt you for a Paragon or Renegade actions depending on the conversation. I chose Renegade just to see what would happen. When I reloaded a point before, I decided to wait it out instead, because I wanted to play a purely Paragon character. I was [i]extremely[/i] surprised that a Paragon action prompt came later on in the same conversation.
I had the preconceived notion that things were either going to be straight Renegade or straight Paragon.
I want those prompts to disappear in Destiny. I want my choices, without foreknowledge of what consequences they may have, to truly affect the way things are around me and in my environment.
This is how I want my Destiny.