First -it's not at all simple -we are nowhere near reverse-engineering it fully.
What does reverse-engineering have to do with it? We only need to recognize how it works.
The process uses the brain's pain function to signal wrongfulness to simple questions (morally) right or wrong? Or, fair or unfair? If it doesn't feel wrong, it's justified.
It signals guilt whenever we remember past moral failures. Essentially, our brains are using the punishment phase of reward and punishment method to train us to become better human beings.
When we do something especially good to help others, we feel good about it. That's the reward phase of the reward and punishment method used by our brains to teach us to become better people.
We agree that our moral intuition is aligned with survival. However, I don't understand your reasoning when you posit that our individual experiences influence the judgments of conscience. Since that would result in different judgments given the same facts involved in the act, how is it possible that the different answers would all be aligned with survival?
Second -it happens quickly, not instantaneously. We have a sort of instinctive conscience and emotional processes essentially encoded into us -which are very complex (along with more survival-oriented processes) - which are increasingly affected by experience and choice/consideration (mind memory as opposed to muscle memory developed with training). Our "immediate" reaction is actually a very quick reaction -but is very much based on/filtered through all of that.
I don't understand how your explanation is possible. The brain is divided into the conscious and unconscious. According to researcher Josh Greene, when subjects consider moral dilemmas, both parts of the brain light up.
It seems likely that the unconscious quickly deals with the two action options and both feel wrong. Then the conscious reasoning mind must weigh the consequences of each to determine which causes the least harm.
If experience was a factor, as you contend, there would be major differences in moral judgments based on age, religion and cultural experiences. Harvard's Moral Sense Test, online since 2003, isn't supporting your position so far.
Intuitive moral judgments are robust across variation in gender, education, politics, and religion: A large-scale web-based study.
http://faculty.georgetown.edu/lbh24/BanerjeeEtAl.pdf