Taken at face value, the parable of the weeds promotes a set of values that are problematic at best and downright dangerous at their worst.
It helps, at least somewhat, to remember Jesus' description of the judgment day when the sheep (the righteous) will be divided from the goats (the unrighteous) in Matthew:25-31-46. There, Jesus makes it clear that the sheep were those who fed the hungry, gave water to the thirsty, accepted strangers, clothed the naked, ministered to the sick, and visited prisoners. Again, taken at face value, God doesn't divide us according to our beliefs or anything else other than our care for people in need. That helps take some of the sting out of the dualism. Mercy, compassion, and care are the measures of salvation and righteousness. An atheist-lesbian-black-female-leftist Arab has as much of a shot at the Kingdom as does a believing-straight-white-male-conservative Christian. That helps.
Jesus' attitudes towards marginal people in general also makes a difference. He had a heart for the poor and marginalized, and he believed that they were the ones who would inherit the kingdom. His standards of measure were again mercy, compassion, and justice.
In sum, there are three things we can do with the parable of the weeds and its explanation. First, we can acknowledge the parable's down side. It can be used to promote injustice, violence, hatred, and prejudice. The parable is divisive and invites misuse. Second, in order to avoid the down side of the parable, we do well to put it in the context of Jesus' "larger body of work" including both his teachings and his ministry with the marginalized. Third, acknowledging the dangers in these passages, they do remind us of the fundamental issue that all of the Bible addresses: human brokenness. The God of the Bible is persistently committed to creating clean hearts in us and filling us with a new and right spirit (Psalm 51:10). While the human Jesus reflected the dualistic heritage of his time and culture, the Spirit that filled him turned his teachings and his ministry in a different direction. It is that Path we seek to follow today. Amen.