I found this solution on Reddit:
Go to control settings, search for ADD FUEL and bind the item which adds 25% to any button. When in a flight, press that control button (a keystroke or whatever you bound it to) and voila, fuel is added! Since it is not possible (to my knowledge) to add more fuel during the planning phase before a mission starts, I think this is ok to do.
To run out of fuel during a several hour long mission is not fun. If we could add more fuel during planning, then I would accept running out of fuel if it is caused by me.