Dear Ryan,
There are two separate contentions made by the atheist here that I'd like to address. The first contention, as you've mentioned above, usually goes something like this:
"If Jesus is God, then why didn't he _________________".
Your example is, why didn't he abolish slavery? The same question could be asked as, why didn't he create a cure for cancer? Why didn't he tell us all about modern cosmology and the expanding universe? Why didn't he create the telephone?
Now, often this type of question puts most Catholics aback and they don't know how to respond. We need to start with why Jesus came to earth. God became one of us, so that we could enter into the divine life through his Passion, Death and Ressurection. An analogy used often, is that God is like a parent. A parent could take a child's colouring book and complete it much better than the child, in God's case, perfectly. But a parent rejoices in watching a child colour, grow, improve, and live. Though every analogy has its flaws, this explains much of the human condition and God's actions in the world and why he lets us act (and really, why we exist at all).
However, Christ does not leave us orphaned to our own thoughts and feelings. He gave us His own example, and the Holy Spirit to guide the Church. Take a look at these two verses in regard to Christ's message against slavery:
"Though he was in the form of God, did not count equality with God a thing to be grasped, but emptied himself, taking the form of a servant" [Philippians 2:6-7)
"He got up from the meal, took off his outer clothing, and wrapped a towel around his waist. After that, he poured water into a basin and began to wash his disciples' feet, drying them with the towel that was wrapped around him... I have set you an example that you should do as I have done for you." [John 13: 4-5, 15].
Because Jesus was both fully God and fully man, he gave us an example to follow, to serve one another but also he came to heal us spiritually. That is why Christ was against physical slavery, but also he came to set us free from spiritual slavery! ("I tell you the truth, everyone who sins is a slave to sin" [John 8:35])
Paul's answer that he is a slave to Christ means that he follows Christ as his master and serves him only (No slave can serve two masters). But it's clear that Jesus wanted humans to serve each other in love; that was His message to love God and to love our neighbour. Jesus gave us spiritual principles to live by, not economic rules.
However, all of these passages from the bible might not be helpful in your discussion with atheists because they don't even believe in the bible. So that brings me to my second contention.
For us, we know that slavery is wrong because of Christ's example (the God who IS love [1 John 4:8]. For us, God (love) is the objective ground of morality. But for the atheists, what makes slavery wrong? Why is it wrong to enslave people or treat them badly? Is it wrong for a lion to enslave a monkey? If we are just animals, why is slavery wrong?
Deep down, their conscience is telling them slavery is wrong, but they don't believe in the conscience so they will have to answer those questions for you. From my experience though, arguments are not the best apologetic especially for the atheist. Always remember that it is not your job to convince anyone. You should pray for their conversion and love them; by doing this you are letting them encounter the God who IS love.
God bless,
Mr. Mathew