Let me begin with the statement that morality is different for everybody. Even in a family everybody has a different morality.
So do I always have to follow the feelings of morality or do I never follow the feelings of morality???
Why so black or white? If you always follow your feelings of morality then you are bound by this rule and can never be free. If you never follow your feelings of morality then you are bound by this rule and can never be free. It depends on the situation, here comes wisdom into play, when to use these feelings of morality and when to use your logic mind.
The question should arise what is wholesome?
So is it wholesome to steal of kill somebody? You can argue that it is just ant-social and that there is no good and bad, so I can do anything, right? Well here comes the morality into play, when you kill someone, it is not wholesome, because your consciousness will hunt you.
When a psychopath kills somebody, this is no big deal, because he has a different morality.
So what is wholesome? Well, when everybody has a different morality then which is wholesome differs per person. (This was an example when you use your ´logic´ to judge, but morality doesn´t agree)
So is it wholesome to feel quilty? Let´s say you scolded at your friend and you feel guilty, is this wholesome? This feeling of guilt comes from your morality. You can now use your logical mind. Yes, you scolded at your friend, but feeling guilty doesn´t make him feel beter, so you can better take action and apologize to him. So is there no meaning to feel guilty? Well, maybe a little bit, it makes you reflect on the thing you did so that you will not likely do that again in the future. So the purpose of guilt is knowing that you did something not really wholesome so that you can reflect on the situation, so you can do better next time and take action. In this case it is important that you validate the guilt because sometimes you feel guilty but there really is no reason to feel guilty. Personally, if I did something without a bad intention and it turns out unwholesome then I don´t blame myself. Knowing that you did something unwholesome is important. But feeling guilty and drowning in it, is just foolish.
So train your morality and wisdom, but also your logic. Meditation is important but it is also important that you can think logical. To use your logic better, I really recommend this course:
https://www.edx.org/course/science-everyday-thinking-uqx-think101x-1I end with what I began with, morality is different for everybody. So really there is no good and bad, there is just wholesome and unwholesome. Wholesome and unwholesome for who? For yourself.