I haven't had a problem with the fruit flies here...except on my bonzai fruit trees, but I don't think they do damage to leaves, stems, soil, etc. Though, I don't know about when they're flowering..Mine are flowering now and the flies haven't caused any harm.
well, do what you can to get rid of them, they can carry diseases(human). I wouldn't do anything to encourage them to stay. They should also die soon due to the cooler weather.
To get rid of pesky fruit flies , take a small glass fill it 1/2" with Apple Cider Vinegar and 2 drops of dish washing liquid , mix well. You will find those flies drawn to the cup and gone forever!