Indeed you can flash it through a serial port instead of USB, but the problem is that you still must use USB to configure it (with LP). Unless...
If you can set one of the ports (Main, Flexi) to be Telemetry, you can configure it with an FTDI through there. You could cut a USB cable and solder it to the CC3D to do a one time configuration and use serial from then on, or just leave the USB cable soldered on (maybe glue it too).
But... Considering it is like $10 or so (shipped) to get a new CC3D, is it worth your time? Better yet, buy a Revo, Nano, or Sparky2 for $30 to $45 and get new features since CC3D is full and doesn't get new features.