You're right - building a dam and waiting for a thousand years will result in a new stable ecosystem with biodiversity comparable to the original. The problem is that natural systems need 'settling time' to adapt to changing conditions. The immediate impact in dams is a dramatic drop in biodiversity, that's not even a controversial claim. It's great that the ecosystem will rebound after I'm dead but I don't think that's what most people are concerned about. Deforestation and desertification of formerly healthy riparian ecosystems isn't a trivial concern. Not all 'changes' in nature are equally beneficial to humans.