Unprofessional staff cost me additional R9000 for single flight

We were three travellers booked on a flight to Cape Town on Thursday 26 October. We did the on-line check in earlier that morning and just went to bag drop off when we arrived at OR Tambo. The queues were very long since it appeared that every person getting served was having an issue or two. When we finally got to a counter, the Kulula woman told us to just wait while she went running on into the masses of passing travelers. Upon her return, she told us we were 4 minutes late to check in our bags. As a result we were forced to buy new tickets and wait 4 hours for the next flight. Nobody called out to the queuing passengers for urgent closing destinations. If this was done, we could have jumped the long queue to avoid the delay. The fact that the Kulula staff member left the counter and delayed us is highly unprofessional. It was as if after seeing our booking paper she needed to delay us so we would have to re-pay. Is this how Kulula is making money these days?