Are solar / geomagnetic storms real risks for commercial aviation?
A pilot in command can always veto, scrub, or divert a flight. Per the Federal Aviation Regulations FAR 91.3(a), "The pilot in command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft." This applies to airline operations (air carriers, FAR Part 121), air taxis and charters (FAR Part 135), and general aviation (FAR Part 91) operations.

A much bigger issue than than the radiation exposure for the people will be the atmospheric effects of the radiation, and how the radiation affects, e.g., satellite navigation. A very strong solar flare can require shutting down some on-orbit satellites to avoid damage—including navigation satellites, such as GPS. A very strong solar flare can ionize the atmosphere to the point it interferes with communications, especially in the HF band used for transoceanic communications.