Depends. If this is a one way trip (i.e. the ticket has no return portion), and you want to get off in Kigali without any intention of continuing to Entebbe or anywhere else on that AP ticket, you can theoretically do that. You don't have the issue of your return being canceled. You have to be admissible to both Entebbe and Kigali.

Having said that, I'm not sure, logistically, how this works on a direct flight with stops. Presumably the crew/GA does a headcount, and if there's a mismatch, they have to verify who's missing (which may involve deboarding pax and reboarding them). I suppose you could tell the FA that you're not feeling to well, so you're going to get off in Kigali and will continue to Entebbe later, but they may not let you leave.. So, I dunno. Theoretically, on a one-way booking, it's possible.