Guilt in nature is something positive. It is an inicator for our own value system. The built in punishment is the artifical part and far spread within our society nowadays. What is left then, if we liberate ourselves from self punishment, judgement, recrimination, vengeance, hate and all that sort of things? I found a possible answer in one of the Seth books.
Quote from "The Nature of Personal Reality" (Jane Roberts / Seth):
"Natural guilt is also connected with memory, and arose hand in hand with mankind's excursion into the experience of past, present and future. Natural guilt was meant as a preventive measure. It needed the existence of a sophisticated memory system in which new situations and experiences could be judged against recalled ones, and evaluations made in an in-between moment of reflection.
Any previous acts that had aroused feelings of natural guilt were to be avoided in the future. Because of the multitudinous courses open to the species, not only did the highly specific nature of many kinds of animalistic instinct no longer apply, but a curious balance had to be maintained. The concious options that opened as man's mental world enlarged made it impossible to allow sufficient freedom, and yet necessary control, on a biological level alone.
So controls were needed lest the conscious mind, denied full use of the animals' innate taboos, run away with itself. Guilt, natural guilt, depends upon memory then.
It does not carry with it any built-in connection with punishment as you think of it. Once more, it was meant as a preventive measure. Any violation against nature would bring about a feeling of guilt so that when a like situation was encountered in the future, man would, in that moment of reflection, not repeat the same action."
Further quote from the same book:
"Guilt is the other side of compassion. Its original purpose was to enable you to empathize on an aware level with yourselves and other members of creaturehood, so that you could consciously control what was previously handled on a biological level alone. Guilt in that respect therefore has a strong natural basis, and when it is perverted, misused or misunderstood, it has that great terrifying energy of any runaway basic phenomenon."