is there any way of flying direct from Oaxaca to Guatemala, or do we need to go back to San Cristobal de las Casas and take a bus into Flores?

I don't think there are any flights you can take. If you are going to Flores, the best route would be to go to Palenque on an overnight bus and make your way by bus and boat via Frontera Corozal. See how to do it in one day without paying ahead and hoping that tour people will really pick you up along the way at:

http://www.mostlymaya.com/Palenque-Flores.html

I did that route from Palenque this past February.