You said some things in this post that I thought you needed answers to.
You wondered why people feel guilty for things they do or don't do. I believe it is because that is the way God made the world. The Bible tells us that everyone knows that God exists. They see it in creation, the feel it in their bones, they realize it when they or someone else does something wrong or right. The fact of wrong or right proves God's existence.
It is not uncommon for people who would, never in a million years, admit a God, to call upon him or thank him when they get into a situation where there is no hope of survival. The old proverb “there are no atheists in foxholes,” springs to mind. People may go into foxholes not believing, and they may come out not believing, but when the actual bullets are flying, the truth comes out.
The reason people look up is because God has made them to look up. God made people to be worshipers. And they worship. They don't always worship God, but they always worship. You can tell what someone worships when you say something bad about their god. You can tell a Muslim when you draw little cartoons of Mohamed. You can tell a Mormon when you make Joseph Smith jokes. You can tell what a liberal worships when you make comments about socialism or how non-progressive progress seems to be.
You can also see worship in the way people who share a god gather to talk about that god. It looks just like church. In fact it is church, it just doesn't worship the God of the Bible. But it is worship nonetheless.
So people act like God exists, even when they claim he doesn't. And this is because he does exist and he made the world in certain ways. Right and wrong are right and wrong because he made them that way. They reflect his character. Reason and logic exist and work because he made them that way. They are characteristics of his. We borrow them from him in our everyday lives, usually without even knowing it.
You mention our emotions. God also has emotions. We are created in his image and that should be expected. We also feel things that we are supposed to feel. We feel love, joy, happiness, sadness, loss, guilt (God doesn't feel guilt because he can't do anything wrong), sorrow, anger, fear, etc. All of these are good and right for us to feel. Our problem is when we pervert them and use then in ways that go against what God has designed them for. For example, it is good to be anxious for the welfare of our loved ones, but it is wrong to be anxious in a way that causes us to think we have some power to control anything. The former causes us to go to Christ and ask for assistance. The latter causes us to try to take control from God and do things ourselves.
Emotions also tell us what we are, or should be, thinking about. For example, fear tells us what we are worshiping. If we fear people we aren't fearing God. If we are fearing God we won't fear man. This is also true of circumstances. I should note here that fearing God is nothing like fearing man or circumstances. Fearing God is more like trust, honor, respect, homage. Fearing man has an element of terror, angst, dread, and loss in it. The reason for the difference is that God loves us and so his awsomeness is tempered by the fact that any reasons God might have to be angry with us have been taken away by Jesus' death on the cross. There is no hope in the fear of man and circumstances. This kind of fear is purely a reaction to a loss of control. God loves us, that big ugly galoot who wants our money, doesn't.
As for brain washing, we all need our brains washed. They are all dirty and nasty anyway. God's cleansing is full of joy and light. He takes our dirt and our heavy load and takes it on himself and gives us peace and real freedom.