For Daoism, conscience is most definitely not the inner light, a reflection of a moral Reality, which leads us to perfection. In the first case, Dao is understood as amoral. It simply "Is" (understanding 'is' as itself a relative, and thus, inaccurate attribution). We might rightly call Dao "Good", but this goodness is not a moral one. Morality, like every human deliberative term, requires its opposite. In Dao there are no relatives.
The morality of conscience, therefore, is a purely human phenomenon and thus subject to the relative vagueness of relative things. Right depends on wrong and wrong depends of right. And these rights and wrongs are all culturally and contextually determined. For Confucius, anything other than a coffin (for a particular class) of so many inches of thickness is right and anything else is wrong. For a Hindu, the same body should be burned on said wood. For a Parsee, exposure to the carrion birds is the proper way. I have picked the ludicrous for my example, but the same applies to questions of murder and patriotism and duty and the rest.
Secondly, because questions of morality are relative, their resolution relies on deliberation. One must weigh the facts as one (quite subjectively) sees them, and then one must decide on the proper response accordingly. Daoism sees this dependence on deliberation as an alienation from something more fundamental to our nature. In deliberating and choosing, one breaks the organic link with what is already true of oneself. In deliberating what is 'good', one severs oneself from the Good. For the Good is what Is, and what Is is your most fundamental 'you'.
Perhaps a good way to understand this would be to draw a parallel between the organ of conscience and the organ of reason. Daoism tells us that reason is a wonderful thing, being as it is, a human thing. Yet the perfection of the understanding is in the realization of its limits. And when those limits are realized, a whole new world of possible ways of understanding opens up for the heart willing to explore them. But, "if we take the understanding as our [only] teacher", we box ourselves into a pathetically limited way of being in the world. Similarly, the perfection of conscience might be said to be the realization of its limits. It is an organ of immense value, and its exercise is of corresponding value; but when we allow it to dominate and rule us, we unnecessarily alienate ourselves from that 'morality' which spontaneously arises from who we are.
The "problem" of the conscience is not, therefore, that we have one and exercise it, but that we do so to exclusion of our substantially wider reality. We box ourselves. The painful burden of an overweening conscience (to which I own up) is thus analogous to the despair of the understanding consciousness which though inadequate in itself, refuses to move beyond itself.
You can check out Scott's other miscellaneous writings here.