The "unequally yoked" phrase, as I interpret it, refers to the fact that you can cooperate with someone who believes differently from you, and they may take advantage of the effort you put in, and take their energy elsewhere to accoplish their own goals which may have nothing to do with your own.
I've been considering what that means in terms of the message of Jesus Christ as we see it in the New Testament. Jesus claims that the greatest commandment is to love God, and to love your neighbor as yourself. (Matthew 22:37-40) So what kind of "unbelievers" do we mean when we say unequally yoked with unbelievers?
Greg's work among Muslims in Afghanistan shows us a great many people who love their neighbors as much as themselves. The amount of energy they put into making education possible for young girls, not just their own families but their whole villages and their neighbors' villages and a neighboring country's villages... really has no explanation I can think of except love. I'd venture to say it looks like the kind of love for god and neighbor which Jesus said was the most important commandment.
Consider, then, if Greg were instead in a church in the United States, and thinking to himself about being unequally yoked with unbelievers. He knows he has the option to build schools in Afghanistan, providing much-needed education for young Muslims in a way that has a powerful potential to prevent wars and terrorism. And to empower people in some of the poorest areas of the world to lift themselves out of poverty, too. (see Luke 18:22) Or he could instead put his money and his time into supporting a mega-church, where church resources build grand buildings, hire employees who'll put their resources into nice cars, nice restaurants, movies, maybe a McMansion here and there, and generally do things that are nice, and pretty. So, maybe, not everyone who says "Lord Lord," (Matthew 7:21) or says they're a Christian, is really a believer in the message of Christ? Who are the unbelievers, and in which situation might Greg be unequally yoked?