I do believe that the church should teach its adherents how to debate with those who are atheist or agnostic. That is not to say that I think that the followers of Christ should take every opportunity to fight with people who disagree with their beliefs. But I think that since it is natural that Christians and Non-Christians bump heads on this topic, the church would be better served if the Christians were well informed on the best ways to handle the trickier questions. Christianity is founded in faith. The Christian church defines faith as believing in something you cannot see. When you are dealing with things you cannot physically touch or see, it is difficult to relay your message to the more science-based minds they often encounter amongst the non-believers.
For any organization such as the Christian church, proper talking and debating skills are highly important when talking to others who may have different views that you. You must be able to get you point across with out starting a fight and causing a bad image for your church by others.
People who exhibit what is being described as having this issue are, presumably, people that have severe issues with Christianity. For it to be to the extreme of phobic, it is to the point of being irrational. There is simply no point in trying to debate with people whose issues are irrational. As debates tend to be fairly negative in nature for many people, it may actually only make things worse.
The Christian church needs to focus on fighting its own battles and leave the lay people to do what they want with themselves. There will always be people who are against religion or against the church but it is not a lay persons responsibility to debate these people. Every person should choose for themselves.
There is no such thing as "the Christian church," there are dozens of branches of Christianity each with their own version of doctrine. But all of them know the Golden Rule of treating others as they would like to be treated. Perhaps if the more evangelical branches of Christianity taught that instead of the raging intolerance they love to spread, there would be less "Christophobia" in the world.