Hi Karl,
Just to clarify for others: using the general purpose pins as analog inputs indeed currently only works at 3kHz control rate.
The _audio_ inputs are sampled at 48kHz.
I think that 3kHz control rate is often an acceptable compromise. In Pd and Max, the default time resolution for events is 4 times slower.
That said, I believe it is possible to ad-convert the general purpose pins at 48kHz, synchronized with the audio clock, but this requires tricky firmware modification, and running them at 48kHz does not mean they 'd become proper audio quality.
You're welcome to file a github issue to keep track of it, but it will not reach my top priority soon.