A small nuke. Something like the old Davy Crockett anti-personnel nuke. If there’s a small enough concentration (like the size of the camp in that clip), something in that range should be able to eliminate any disease. Ebola is a finicky little bugger, and needs very specific conditions to exist. A high dose of radiation would wipe it out.
what if the locals object to being nuked? I guess they don’t have a choice in your world...