Given a well-formed conscience, guilt is actually a pretty good guardrail against bad acts. The intellect has to be the ultimate guide, but the gut feeling of guilt can kick in and give us a warning when we don't have time to deliberate.

For what it's worth, I don't personally think smoking is the worst thing. It's damaging to the health, yes, but so are a lot of things, including, say, alcohol and sugar. Arguably, smoking, drinking, and sweets also have their benefits as well. The key is moderation. The bigger problem with the cigarette addict isn't that he is engaging in a damaging habit, rather, the bigger problem is that he is an addict, that is, he is unable to moderate the habit. The same applies to the drunkard: his enjoyment of drink isn't the problem so much as his inability to control it.

This is why I am so convinced of the value of virtue ethics. Assuming our instincts are relatively healthy (not always the case, they can become damaged), then it is generally good to partake in that which we enjoy. However, partaking in excess, or rejecting the good altogether, are bad extremes. Enjoying a drink or two on occasion with friends, for example, is a good act, done for a good purpose, done in moderation, and with a positive outcome. Smoking a pack of cigarettes a day by yourself is an act done in excess, with a negative outcome. Maybe smoking a single cigarette on occasion, in a social setting, could be a good act. There are always a lot of factors to consider.

Obviously there are cases where the act in question is more serious by nature, such as murder. Having a smoke could, perhaps, go either way, but some acts, I think are always wrong.