I don't think that leaf cutter bees are a real problem, but it would depend on how much space the bee needs to construct its nest tunnel. It might cut through the roots if they are in the way.
I agree that it would be a shame to kill them, so I guess that somehow you need to develop a barrier between the open air and the soil, so the bees are no longer attracted. You could do this by, perhaps using pots with only holes at the bottom, and put a good lining of stones at the bottom; and then leave some space, maybe 1-2cm at the top of the pot and fill this with grit or gravel.
I don't know if this would work, as I haven't experienced this particular problem, but it would seem to me to be a deterrent - I hope the bee would think so too!