I would disturb the soil as little as possible. Just cutting the plants that you need to remove off at ground level, and digging small holes for the new transplants, or planting seeds in spaced groups, rather than rows. For plant health, that will require a good coating of mulch, but I don't know how that would affect the bees. I wouldn't worry to much about being stung, though--solitary bees like these normally don't have stingers.

I have these residents too and I feel really guilty when I do any weeding, then see a bee frantically searching for it's hole which I have disturbed by weeding. Unfortunately we just can't leave all the weeds in the flower beds (or veg beds) so I try to work round them, but sometimes (here anyway) the weeds are too thick to notice a small hole in the garden. Our grass is often littered with thin sticks showing me where the bees nests are, it also helps them to orientate after you have cut the lawn - bit like a house number!
Sitting digging buttercups out of the lawn over the weekend (easily amused me) I noticed some insects buzzing around and assumed that it was the ground bees, only to find that we actually have a wasp nest underground as I watched several disappear into the grass. Even the wasps are usually OK if you leave them alone, but they do get a bit touchy about September time - knowing (or not) that the majority will die soon!

Whether they know that or not, they do know that they need to protect the young queens--their sisters--which will start new nests in the spring. Aside from that, they are also beneficial, eating many pest insects, especially caterpillars--spare them if you can!