I think the issue is solvable for continental flights, but it becomes really difficult for international flights. At least not unless you get others to also support it, for which many sadly wont have any incentive.

Want to tax the whole distance rather than just the portion flown within the airspace you control (which will be minimized as much as possible)? Airlines will split up long distance flights by utilizing airport hubs just outside your jurisdiction. Giving those a major advantage and moving a substantial business away.

Combat this by taxing on an airline level? Airlines will just split into two entities, one serving europe and the other the rest of the world. Again leading to a loss for your economy. And at least for long international distances there is no alternative to flying.