There is a switch in the audio output port that tells the Mac if you have inserted a plug. This switch disables the internal audio when a plug is inserted. The rusty port very likely had a malfunctioning switch in it.

One or two of the pins in the port are hooked up to this switch. Have you checked to see if you have internal audio now that you have removed the ports? It won't hurt your Mac to run it without these ports, so long as you make sure that your solder is cleaned up around where the ports were and not shorting anything. You could probably replace the ports with the ones from your old CC board, they're probably the same.