I'm not sure how externalities should be priced, but it does seem like a good idea, especially in the age of climate change. It is likely politically and practically very difficult though.
France are I think effectively banning internal (non connecting) flights in return for the airline bailout. Most of the night trains are international, but the EU could ban short non connecting flights overall too at some point.
Don’t most airlines already offer to buy carbon credits to compensate the flight at a minimal price? Accounting for all other externalities shouldn’t make flight much more expensive.