The Tips and Notes on the introductory lesson says that doubled vowels should be pronounced long rather then separately. So, I'm guessing it's ''waafreeka''.
I thought that's what he meant when he said Wa-afreeka, but you're right. I misunderstood his examples :p
Phonetical description hints that hiatus (a number wovels in a row) in Kiswahili is eliminated with kinda "glottal stop" - which slightly separates these two (in this case) sounds.. so i'd consider it as two separate sounds which can lazily! be pronounced together.
When you speak slowly ("correctly") they are separate, but as you speed up, they merge a bit, but remain longer than simple a-s. Does that make sense? :)
Maybe this will help;
singular: mwafrika = mw + afrika,
plural: waafrika = wa + afrika