Data point - a correspondent on Fodor's just tried to book out of WDH using the online tool (from the USA) and it hangs at the payment screen. In this case BA would be the issuer as the first flight (WDH-JNB) would be on BA/Comair.

I suggested they look for a TA in Windhoek that has GDS access; hopefully there's one that could issue the ticket in a similar manner to the one who JonNYC found in Joburg.