I am not sure what the issue is here? If it feels wrong to play a character a certain way, then simply don't do it. If it bothers someone that others might play a character contrary to how they think they should be played, then maybe don't watch play videos or play the multiplayer with people that don't think the same way. I think this would probably be the safest way to not be bothered by how other people play their game. Most likely companions will have different dialogues for situations that will be based on how they are "supposed" to be, but all the options will still be there to take the different paths and for corruption/redemption stuff.
I think the Origin system is not going anywhere, they have spent too much time on it already and while I may not play as one myself, I am glad it exists. Many people seem to have trouble in coming up with backstories and feel "lesser" than the companions, and some people don't care about creating a character at all and just want to play the game. Origins make it easier for these people.
