Yes, once you've completed the requirements for the retail option, you can go ahead and sell the store.
To be honest, I don't know how much of a problem culling could be. My experience has been that sims in houses don't get culled, but other people have had that happen. I tend to keep my households fairly small, so I'm probably not the best person to ask. The team did decide, though, that if someone has a household culled from their game, that it wouldn't be necessary to occupy that lot a second time.