be careful if combining buddy passes and paid flights. On the way there, assume you won't get on the plane on the first day and have couple days built in at your connecting point (AMS, JNB, etc). This is especially true if you are going in high season (summer for europe, winter for SA). On the way back, you can buy a piad ticket since you are getting TO you departure point with Delta. If JNB flights look ok, I'd go with that. When i looked in the past, very often price of ticket Europe-East Africa was sthe same as NA-East Africa, so no point using buddy passes.
If I were you, i'd look on the map where Delta goes and pick the most interesting, far away place you can get to on Delta, without complicating it with additional tickets (except maybe very cheap local short-hops that you can throw away or change without too much $$).
My #2 option would be to use miles/award tickets for the 2nd leg. This way, if you misconnect, you can either change or redeposit miles for a known max cost (sometimes free if you're elite).
If you want beach, i'd look into flying to JNB, spending some time in SA (cities, safari, whatever) and going to Mozambique. Equally bueatiful beaches. Not as much history as Stonetown, but most people don't go to Zanzibar as a destination. Most go there as a rest stop after safari in Kenya/Tanz.
Also ask about embargo date, where no buddy pass travel is alound, regardless of loads.