I don't pave over the stones, my paths just lead into the stone then stops. It doesn't look super unnatural. In front of entrances, I just wrap my design around it so it looks like it's hugging the empty spot.
I use paths that can come to an end using corners and side pieces and lead those to the blue stone in front of buildings. It doesn't look the best, but it looks more natural to me than trying to pave over the blue stone.