However, a major problem is that legislation tends to protect rare species instead of rare genes. (The laws are based on the traditional view that hybridisation is a rare process that always results in one genome completely swamping another) (Bridle, 1997). This is rarely the case.
Hybridisation is a major problem in safeguarding protected species. Often, hybrid animals are not protected by environmental law, even if they appear to be identical to the pure animals (Ibid). In the US, the 1973 Endangered Species Act only protects animals that have not been 'contaminated' by foreign genes. This means that the funding to protect American red and grey wolves is threatening to be withdrawn as it has been found that they have interbred with coyotes.
Although all animals are important, unless they are found at the top of the food chain, it will be relatively hard to protect them due to predation. (For example, the Black stilt in New Zealand. This rare wading bird is currently under threat from ferrets, stoats and feral cats) (Anon 1997). Maybe it is more important to try and preserve diverse habitats than actual species. As you say, what is the point in preserving an animal when there is no habitat for it to return to.
References
Anon. (1997) Birds on the brink. NEW SCIENTIST NO. 2009
Bridle J (1997) In the name of purity. NEW SCIENTIST NO. 2097