You can do it already, just run JACK with a plughw device rather than hw.
Cool!
But, why do you want this? You'll get better results running at a hardware supported sample rate then resampling at the end.
I have sources that were recorded at 48kHz. I figured that if I downsampled before mastering the processing would possibly obscure the conversion noise for the finished product (CD), at the cost of having conversion noise during monitoring.
Thanks for the tip! Carlo