If a black hole were discovered flying toward the Earth and was predicted to arrive in five years - a scenario which I believe to be scientifically plausible, though - whew! - unlikely, the question is what we residents of planet Earth would do. Obviously we'd scramble to figure out the best approach to keep homo sapiens and all other surface life from going extinct. We might not have a perfect answer, we might not be able to build a perfect closed ecosystem - but we wouldn't have a choice. Yes, there would be social disruptions, but those can be good fiction material.
I don't believe that allergies would be a big problem, because the cities would be fairly large and well populated. Plenty of allergens floating around to exercise the immune system.
I agree that structures could and would be built above ground, but underground would provide better insulation and would be easier to protect against meteorites when the atmosphere is gone after a few years. Seems to me that heavy equipment - bulldozers, backhoes, excavators - could dig large cities fairly quickly and efficiently compared to conventional aboveground construction. Sink posts, pour concrete, lay beams and joists, build roofs, cover with soil, and you'd have an enormous interior space within which you could construct streets, apartments, shops, hospitals, theaters and so on, as well as hydroponic farms, livestock barns, science and engineering research labs, and manufacturing facilities.
Keep those objections coming. I want the story to be scientifically credible, and I certainly haven't thought of all possible complications. By the way, I will look for that Meela's Flowers short story you recommended and hope to learn something from it. I will point out, however, that an approaching black hole is somewhat more believable than an advanced extraterrestrial society warning us that they plan to destroy the sun.