When did you purchase the ticket?
There was a significant rule change that came in the with the 22-Apr-2016 version of the rules which is relevant to your situation - I'm assuming here that the issue your airline has is that you have stopovers in Europe/Middle East both before and after your trip to Africa (LHR and JTR before JNB and DOH after)
If you purchased the ticket on or after 22-April-2016, then yes your ticket is invalid
But if purchased before that date, then the ticket is valid
The relevant rule before 22-Apr-2016 stated, in part:
4(e) Only one intercontinental departure and one intercontinental arrival permitted in each continent except as follows:
1.
2.
3. Special provisions for travel which includes Africa:
For travel originating other than in Africa one of the following backtracks is permitted:
3.1.1 Europe-Africa-Europe
One of the visits to Europe must be a transfer without stopover between Africa and the previous/next continent.
Travel may not include Mauritius/South Africa
3.1.2 Middle East-Africa-Middle East
One of the visits to Middle East must be a transfer without stopover between Africa and the previous/next continent.
3.1.3 Europe-Africa-Middle East or Middle East-Africa-Europe
Travel may not include any flown or surface sector between Europe and Middle East
Your itinerary satisfies 3.1.3, and it does not require one of the visits to Europe/Middle East to be a transfer without stopover (unlike 3.1.1 and 3.1.2) and therefore you are allowed the stopovers you have in your itinerary.