Elevate the stores.
The cost of that is immense. Why not just make the surface (ground level) street more accessible to pedestrians, and keep the businesses where they would prefer to be?
Aren't there large parts of Chicago already like that?
Chicago is also somewhat of an exceptional city in this regard in that it was to an extent demolished and rebuilt twice, and the city was further built up from water level to accommodate underground plumbing and (IIRC) to reduce the swampiness of the land.