There is a great video showing how the MC goes from being clearly defined right and wrong to becoming a more of the 'right by him' and at any cost necessary which makes him act just as wrong as many villians.

Thats why the battles now between humans become less aparent and learning the titans are humans and weapons as well it become even less clear where the line for right for freedom vs is ok to kill.

Please check this video is very good on the whole issue: