Was in Southern Africa last May. Completely independent travel. Rented a car and drove from Cape Town to and through Namibia. Flew to Jo'berg and then drove to Swaziland. Both South Africa and Namibia are easy places to travel. I'd say as easy as Europe. Cape Town is filled with police and tourist police. We didn't go to Jo'burg or any other major city in South Africa. I wouldn't walk around after dark and I'd check with the hotel before going to any non-tourist area. I really did feel safe. (I'm a 65 year old female.)
My bias is to local travel agents. My experience has been that it works out to be about 50% of the cost for the same trip as with a US agent.
So, would you rather work with someone who may have never been where you are traveling or work with someone who is on the ground in the area where you are going and can make real recommendations? I've found that even the big tour companies, often the person you are working with has never been to the country and is relying on an incountry agent for info.