Interfacing Atmel Processor with i2s codec
Whether that's a problem depends on how you use the audio.

If the sampling rate of the original audio is 44.1kHz, but you use 12M/256=46.88kHz, the audio will be higher pitched by around 6%. You can check how this would sound via Audacity or similiar software. 

However I don't really get why you think that the I2S would be tied to the processors frequency with a 2^N divider - you could just use a timer with a divider closer to the needed value and since the main clock for a S70 is up to 300MHz, you could just divide that by 6803 by using a timer and get a 44.098kHz sampling rate, which has an error of only ~0.005%.