The thing about Skyrim is that it portrays the idea of a Nation divided very well.
Whatever choice you make,on one end you will always make a bad choice.
Someone will always be unhappy.
Sometimes there simply are no 'good' choices to be made,or not even any middle ground to step on.
Quite often there will only be the lesser of two evils.
Life will force you in many ways.
Storywise,the Molag Bal quest was similar.
When Bal ordered me to kill the npc i walked in with,i had no such desire.
It was simply the NPC's foolish and weak response of 'i have to kill you to live myself',that forced me to defend myself.
The Good option in that situation?
Die so that the other might live.
That how you wanna play the game?
As a bandit one would think i could hang with other lowlifes in their camps,but they see me as an enemy and attack me,so naturally i have to defend myself.
You join the Companions,get forced to become a Werewolf,but never use its power.You didnt even kill a single soul in your initial transformation.
Do any of these choices make you inheritely Evil?
Life throws a lit of [censored] at you,its how you react and what do do with the options that are GIVEN to you that define who you become.
Like stated before,in a Civil War where both sides have an equal and fair point of view,you can never make 'the right choice'.
If you cant comprehend that concept,i'm afraid there's little more to be done than a bullet to the head.