I did 2 weeks in Madagascar with a t1i, 20mm/2.8, and 100mm/2.8 macro. The 100mm L did not exist yet and I was too broke and hell-bent on moving to full-frame, or I would have gone for the 17-55 instead of the 20mm prime. I also threw the 18-55mm in my bag as a last-minute back-up, but almost never used it. With that in mind, here are my thoughts:
You should bring a standard zoom. You will want to take pics of everything you see, at least at first, because the cities, countryside, and people are all very striking, dramatic, and photogenic. For me, I made do with the 20mm (32mm equivalent), but the zoom would have been better.
You should bring a second body. The lens changes did make me nervous, and we traveled during the dry season. It is quite dusty, everything came back with dust on it. I felt like Pigpen on the flight home. If you travel during the rainy season, I think you'll face moisture and dust.
I wouldn't worry tremendously about the zoom length. If you put the 70-300 on a crop body, I think you'd be thrilled. You could swap out for the 100mm if it is truly dark and get 160mm 2.8 with IS, and that would probably do quite well. We did not do jungle- or wildlife-type excursions, we mostly went to little zoos or parks where the animals were mostly tame. The 100mm served well for that, although the flexibility of a zoom would have been better. I did not really need the close focusing of a macro, I was not a big flower guy, and I had no intentions of hunting for bugs. I chose it for the quality and the 2.8.
If I were to go back today, I would have my 24-70 on the 6D almost full-time, swapped out only for the ultrawide, and then have the 70-300 or the 100mm on my cropped backup. I would not worry about low-light much, unless you have some night excursions already planned. When we went, dinners were long (to allow the kitchen time to procure the food you had ordered), and then straight back to the room for showers and bed. Because you will be TIRED. This country is extremely tiring, everything is hard work, even a car ride. Also, the mosquitoes (malaria) and just overall safety/security are concerns at night, so you probably won't be doing a lot of nighttime shooting.
Overall, though, pack as light as possible. I carried all my gear with me in a very nondescript black belt bag (not a photo bag) so as to avoid attention. When I wasn't wearing it, my gear bag was locked in a suitcase. If you wear a backpack, it will end up in the back of your van and frequently getting carried by "helpful" folks looking for a tip. I'd go for a shoulder or waist pack that you can keep with you in a cramped moving vehicle.
Note -- we were never in any real danger, but we traveled half our time with two missionaries who had lived in the country for years and spoke the language. We stuck out like sore thumbs (four tall white people), and a tour group probably sticks out even worse.