What *exactly* happened to Zaf?

[JHyde]

That was what happened. The burned bodies were the men who took him and were in the van with Adam earlier on, to whom they gave the fake vaccine.

The Redbacks then kidnapped Zaf from them, burned the original kidnappers and left them where Ros was to find them and set off with Zaf. Presumably they got hold of the vaccine/antidote on their lonesome, which was how they were able to hold and torture Zaf for months, the whole of season 6 (I think about 8 or 9 months in total).

Hope this helps.