I must respectfully disagree. If you are not used to driving a stick, and you are also not used to driving on "the other" side of the street, a manual transmission is, to me, a giant pain. We have been going to Kruger every other year for a decade, and spend almost all of our time on dust roads, and I HATE having to manually shift. Slamming that thing into reverse when an angry elephant wants you going the other direction is a nightmare...to me. Yes, we have done it, but it is not ideal. I agree that you should contact the Skukuza Avis folks directly and try to get an automatic if you can. You will survive a manual, but for these trips of a lifetime, go for what will be the most comfortable.
You have made several good points, and I would agree that driving a manual can be a major hassle. However, I can't imagine anyone driving through Kruger is going to need to shift into more than 3rd gear, and there won't be a continual need to shift up and down and all around as we must in city/suburban traffic.
If the OP is driving only within Kruger then it truly won't be difficult to navigate on the left side of the road.
Granted, driving an automatic would certainly be easier, and more costly, and noisier when in park or neutral (fan going). There are pros and cons. I would never want my mother (75) driving a stick shift, but my husband (67) and I (53) are both fine with it.
Staying within Kruger an automatic is great, and I would definitely do it. Outside of Kruger, in any rural location or on iffy roads, I would think a stick shift would be much better. On my last trip it got me out of some really tight spaces.