I had a similar issue (award booking, but just LHR -> JNB -> LHR). Virgin said that I could have a rebooking to a different day (but only within 24 hours) or a refund. I asked about the rerouting to AF/KLM, and was advised that if the route was flown by DL, they would rebook onto the partner flight, but as DL didn't fly it, the only options were a redate or refund.

It may have been an agent unfamiliar with the partnership with AF/KLM, it may be that the partnership is still only part formed, or it may be that the rerouting was not identical (2 legs instead of non stop). However rather than debate, I took the option of switching to the day before out, day later home, which worked for our plans. Ultimately we didn't fly, we were in the lounge at LHR when the change in travel regs to South Africa was announced and opted not to go. That, however, is a different story.