Depending on the conversion time, switching between an A4->A0 sequence and a single A12 conversion may take more time than sampling through the superfluous channels in a single sequence.
However, during sampling of these unwanted channels, the ADC may disable the digital I/O pins for the sampling period (see the port pin schematics of your MSP). This may affect your external hardware. In this case, you don't have any option but to switch operating mode.