I have had the same problem with the JHB-KMIA flight but one time they were absolutely firm that I couldn't take my camera bag on board with me. I told them it was cameras and they didn't care. Finally they let me bring it in, but I couldn't have it at my seat and the flight attendant put it in a closet at the front of the plane. I didn't take my eyes off the closet the entire flight!
We always fly Virgin Atlantic SF-LON-JNB. I love the airline but the maxium weight for an item of cabin baggage is 13lb / 6 kg!!! Camera, case and 100-400 will do that! Once there was a woman with a scale in the boarding area and I almost had a heart attack!
Love that Kata bag (work of ART!). Last trip I went with a Nanuk (like a Pelican - HARD sided) and it worked out pretty well. It looks small and doesn't raise any eyebrows as you are checking in. If something LOOKS heavy, you can be in trouble! I can fit in 2 bodies, 10-22mm lens, small mac laptop, small external drive and a few other things. I put the 100-400 in the bottom of my purse. Husband gets one other lens, chargers, ipad, binoculars and other little things. We don't have any room for much else. I am a big believer in NOT putting anything in the check-in that I can not live without. There are too many can't-live-without camera/electronic things!
I agree that the tripod is a huge hassle. I wish there was a small, lightweight one that was really sturdy, but I have never seen one. We go for the beanbags (the kind with 2 legs that fit over the door) and I have been very happy. We fill them with buckwheat hulls. I tried beans and rice once, but the bag was so heavy I couldn't pick it up. The beanbags and all of the backup items (extra chargers, extra cords, extra...) and the cheapo binoc go in the checked bags.
I am soooooooooooooooo ready to pack, but April is a long way away. Too long.