Flash can be used, albeit subjectively. There is still much controversy over proper use of flash in nature photography, especially for subjects like birds. Sometimes fill flash is needed to lighten shadows and give a better colour and a catchlight in the bird's eye. Usually bird photographers use a Fresnel lens device (see below) to help focus and "throw" their flash beam onto a smaller area over a longer distance. However, I have seen nature photographers abuse this by using Fresnel lens even when the bird is say less than 5-6m away or as in the above case mentioned by TS. The intense flash power strobed continuously for over several seconds at close range may be too overpowering for the bird in question, and may cause undue stress and disorientation.
There is high chance the nesting may fail if there is too much disturbance from human behaviour or activities which might cause parent birds to abandon the nest or chick, and the chick may starve to death or eaten by predator as a result.
Education can only do so much....that is why it is important for the veteran nature photographers to practice proper ethical behaviour in the field for newbies to follow...but if everyone cares only about getting a nice shot at the expense of subject's welfare, as seems to be the current trend now, then its a very sad world we live in indeed.