I agree it is difficult to be black and white about cloning. We generally encourage people to shoot Raw and post process for better results, which immediately and deliberately introduces an element of intrusion into the final result. How far this is taken should ultimately be up to the photographer, but equally it is a matter for the relevant web site as to whether it is deemed acceptable for that web site (or that competition etc).
As Ian notes BLP accepts 'minor' cloning of distracting elements. For a website such as BLP, which has a strong element of conservation, I would suggest that images for the Main Library err towards accuracy of the scene rather than manipulation (this is my personal view, not necessarily a BLP Committee view). Presumably what we are trying to achieve generally is accurate depiction of the bird and the environment in which it lives. I would also suggest that disclosure occur, probably in the Comments box, to indicate that some cloning has taken place. This would not be intended on passing any judgement on the process, but merely for future reference such as if a conservation organisation wished to use the photo at some later date. The BLP website caters for other images through (for example) the Creative Images gallery, where members can place images with any amount of alteration, conversion to black and white etc, and this gallery is probably under-used. That said, I have submitted images with minor cloning on occasion particularly in situations where there are distractions on otherwise smooth backgrounds such as reflective water.
Its probably worth acknowledging that even if you don't clone, you can still use raw processing to make quite significant changes to the 'look and feel' of the photo. For example I would think it is relatively common practice amongst BLP members to work on photos to bring the bird subject more into prominence and blur the background either using heavy noise reduction or blur tools in their favourite processing workflow. Likewise even if you don't clone you can still use careful local adjustments using adjustment brushes to considerably reduce the impact of distracting elements in the background. I think a risk that comes with powerful software is that we try to resurrect far too many poor photos that are better consigned to the trash can (I put up my hand to this!). In the case of the photo attached to David's post, if it were mine it would be a 50/50 call as to whether I tried to fix it or just accepted it as a miss; there is a subjective and blurry line as to whether one should just accept that one didn't do a good enough job with camera. But that's just a personal perspective and I am still learning about what makes a good bird photo. As an aside I notice that the rules of the BLP's Australian Bird Photographer of the Year comp specifically disallow blurring.
Cheers
Simon