No it doesn't. A guilty conscience is not a work of the intellect at all but is a classic example of innate morality at work. And the ultimate end of atheism being nihilistic is dictated by the fact that there is objective basis for morality under atheism. That Rand does not have the courage to follow her philosophy to its logical conclusion is of no moment.
If you argue that the intellect doesn’t determine morality, you must either argue that man is born with a fully formed sense of morality, or that it is divinely revealed to each and every person.
Please provide evidence of either.