In order to help prevent terrorism from spreading rapidly across the globe, everyone needs to be more proactive. By giving easier access to all of the states on the African Union, it is just growing the potential for terrorist groups to more easily cultivate their ideas in areas where they formerly had no less access. Monitoring where and when people are traveling will give us insight before negative situations occur; whereas, a common passport will allow for terrorist problems to begin and grow, possibly without being noticed.
Yes, if the African Union issues a common passport to all 54 states in Africa, it will hurt the fight against terrorism. Certain states in Africa have been decimated by terrorist groups and are run by them. With visa-free travel, these groups may be able to spread like a disease across the remainder of the continent.
Cooperation among nations - like free trade agreements - is important to promote peace and prosperity around the world. However, countries need to be able to control their borders and immigration so that they know who is entering their countries. Terrorism has been on the rise in Africa. Therefore, the African Union's proposal to grant visa-free access to all of its member states will hurt the fight against terrorism in the continent.
The common passport will require people to go through the same background checks as before. It will simply streamline and standardize the process. It may even mean tougher background checks on people who traveled from countries with weaker requirements. This could actually help fight terrorists, by making checks stronger than before.