His willingness to let Sera get hurt to maintain his cover cemented his position as a terrible person in my opinion long before he truly went off the deep end like he is now.

As for Arlo, he's much more of a product of his surroundings as anyone. If you're willing to make excuses for John I don't see how you can not do the same for Arlo. He's spent every moment of his life being brainwashed by his family, friends, and even his government that maintaining the hierarchy of power is the best thing he can possibly do for people. The fact that he's as open minded as he is is already borderline unbelievable.