I was recently deemed "undesirable" in South Africa for overstaying my visa. I want to visit my South African fiance in Botswana but all of the affordable flights stop at OR Tambo. Will the gate agents for my connecting flight before SA know I am not allowed in the country and prevent me from boarding? I don't want to get stopped in London/Zurich and not have Christmas with my fiance.
Also will the gate agents in my connecting flight before SA know I am not allowed in the country and prevent me from boarding?
No they will not, as South Africa doesn't do advance passenger screening.
Unlike most countries, South Africa does perform "border" control for transit passengers, but as you're not trying to entering the country, not much if anything will happen.
So you should definitely be fine.