Josef Loessl: How bad is Augustine's "bad conscience" (conscientia mala)? An enquiry

Augustine's concept of moral conscience follows an earlier Christian tradition which is based on an exegesis of Romans 2:14-16 and passages such as 1 Timothy 1:5: con-science as the manifestation of the law of nature "written into the hearts" of all human beings and enabling each to know and to do what s/he ought to do (the good) and not to do what s/he ought not to do (the bad). This "good conscience" (conscientia bona) is manifest in principles such as the Golden Rule or the commandment to love one's neighbour.
In the context of his teaching on Original Sin, however, Augustine transforms this concept of a positive (rational and volitional) faculty into one of a negative (guiltlike) emotion (conscientia mala) that "reminds" people of their inherent sinfulness. In this context he advises people to "use" this emotion to acknowledge their need of forgive-ness and to ask for God's grace, which would restore their good conscience, which in turn would cause them to do good works.
This account of moral conscience raises some questions, such as: Is conscience a rational faculty or an irrational emotion? If the latter, then what is it that provides the conscience with reason and volition? If the answer is "grace", then what is the role of the natural order and the law of nature? And how is for human beings trying to do the good thing and to live the good life related to salvation?