score:6
The cheapest way to get from Europe to South Africa is, easily, flying. Booking and flying at the right time can easily get you a roundtrip for under 800 USD, sometimes even less.
Not taking into account safety, nor taking into account additional costs for simply being in transit (that is, food and accommodation), just the sheer cost of all the visas you'd need for traveling overland through Africa will already make up a significant chunk of that 800 USD. And, if you're from the 'wrong' country, the total visa cost could even exceed 800 USD.
Then, the distance you'd have to travel overland is, at best, some 10000 kilometers each way. Even with the cheapest forms of transport, this will cost you several hundreds of dollars, in each direction.
So, the total cost of flying will be less, if not much, much less, than traveling overland.
Upvote:0
I strongly recommend flight, which is usually via Johannesburg. Cape Town is safer than other places in South Africa, and in general South Africa is safer than other countries in Africa. Don't put your trip in risk in favor budget. Africa can be safe and dangerous, and there is no guarantee for neither.