Interesting view point. Are you sure that your good conscience is not from an external supernatural influence? And if you are sure, how do you know this? I cannot disprove your theory. I also cannot disprove that invisible faries don't control the fate of the universe, does that make it true?
Unacceptable to who? Majority rules in society, you know this. And what happens when we ignore this internal warning system? It's called guilt. Should we be punished? it depends on the offense. And who should punish us? It depends on the offense And whose standard do we judge by; your internal warning system, or mine? Majority rules, as stated before And what is to say your internal warning system should be a moral absolute for my internal warning system that differs from yours? My internal warning system is not yours, everyones system is programmed by their parents/surroundings except in cases of sociopaths. Parents teach what they know. Society guides the knowledge of the parents.
And if today 95% of the people do what they feel is right, what happens tomorrow when they no longer feel it is right? You feel "guilt" You cannot change the past, what are you asking?
My point is this: If we ignore an absolute authority for what is good, and what is bad, we then become that authority. We have seen what man is very capable of if left to his own internal warning system for what is good, and what is bad. He will justify murder when it suits him, and condemn it when it does not. He will steel to keep himself satisfied, and condemn the same when it is taken from himself. So maybe it is an external supernatural warning system that should receive the credit for what is good, and what is bad, and not an internal system. If that is truly what you beleive, you're also saying that protestant religions are bad because they changed the way things were originally intended to be? The simple fact is that people changed god to suit themselves better.
The word of God does speak on the subject of conscience, and to whom the conscience comes from:
Rom 2:12-16:
For as many as have sinned without law will also perish without law, and as many as have sinned in the law will be judged by the law (for not the hearers of the law are just in the sight of God, but the doers of the law will be justified; for when Gentiles, who do not have the law, by nature do the things in the law, these, although not having the law, are a law to themselves, who show the work of the law written in their hearts, their conscience also bearing witness, and between themselves their thoughts accusing or else excusing them) in the day when God will judge the secrets of men by Jesus Christ, according to my gospel. NKJV