Because all these disease associated genes have functions, we can't just knock them out, they have important work to do. The disease associate variants are just that, a variant of a healthy version of the same gene, which could be all sorts of different things, too much/little expression (Crispr won't do anything here), or a mutation that changes the protein (Crispr might do something here with a lot of additional tinkering).

The other problem is delivery. It's relatively easy in a dish, but doing it to every cell in the body is essentially impossible. If the disease exists in, or can be fixed by modifying, an accessible cell type like say circulating immune cells, then that's the first target for medicine. See for example car-t cells.