Assuming the airline does'nt have a problem, is it better to daven alone or with a Minyan on a plane, where the latter will cause discomfort to other passengers? Could this cause Chilul Hashem?

The Minyan on the plane is already an accepted phenomenon that is recognized by seasoned travelers. I don't believe it should cause problems of Chilul Hashem. In general, the Minyan is located where it interferes as little as possible with others.