How should I deal with feelings of guilt?
Guilt means we're aware of a gap between what we do and what we should do. As long as we don't live up to our ideals, we'll feel guilt. To be free from guilt, either we must live completely according to our accepted standards of behavior, or try to lower our standards.
Lowering our standards isn't recommended for those on a progressive spiritual path, because it means lowering our consciousness. Animals, for example, have less developed consciousness than humans; they don't have the sense of right and wrong that humans have, so they can't commit "sins." For them, there's no karma. But human beings—along with having higher consciousness—have a higher degree of responsibility for our actions. When we do something wrong—against accepted codes of morality and ethics—we feel guilt, because we know better.
How we deal with our guilty feelings determines whether our consciousness is elevated or degraded. We can choose to make amends—acknowledge wrongdoing and try to improve—or we can abandon our human responsibility, ignore our higher sensibilities, and respond to guilt by decreasing our standards. Some attempt this through intoxication or other consciousness-lowering behavior, with the result that their consciousness becomes increasingly animalistic.
The progressive route is to simply admit our offenses, pray for upliftment, and abandon behavior that goes against our ideals. Guilt is a helpful indicator that we still have progress left to make toward our life's perfection. We shouldn't let guilt immobilize us or frustrate us to the point that we give up trying to make amends. The path of spiritual progress includes learning from our mistakes. Learning can be painful, but such pain is meant to correct us and protect us from future suffering.
As the sixteenth century acharya, Srila Rupa Goswami writes, "There are six principles favorable to the execution of pure devotional service: (1) being enthusiastic, (2) endeavoring with confidence, (3) being patient, (4) acting according to regulative principles, (5) abandoning the association of nondevotees, and (6) following in the footsteps of the previous acharyas. These six principles undoubtedly assure the complete success of pure devotional service." (Upadeshamrita 3)
So we have to be patient and persevere. As long as we stick to the process of Krishna consciousness, our success is assured.