The factor in question, naturalness, is actually being used incorrectly at this point, I feel. Something which is unnatural is that which is not bounded by the laws of nature. It is effectively the same as what people mean when they say supernatural. Therefore, anything that can be known about with the five senses is natural and anything which cannot is not natural.
Additionally unnatural has come to be used to describe that which is not intended by nature. Nature, in this case, would be things like evolution, the big bang and other creative, scientific theories that have, in some way, affected humanities development. For example, some people argue that homosexuality is not an effective way of passing on one's genes and therefore is unnatural because evolution cannot have produced it. However, such a view is spawned from a misunderstanding of these natural laws often with many semantic errors such as take the phrase "intention of nature" too literally and subconciously, mistakenly, assuming that it implies that it is possible for such a thing to have an intention.
Homosexuality is clearly not unnatural under either of these views. In fact the only definition under which homosexuality is unnatural is the following: Unnatural, that which pertains to or has relation with homosexuality. This final definition is the definition most often used by those who describe homosexuality as unnatural. However, doing this brings no additional meanings to homosexuality than if I were to redefine the term "toilet-paper" to describe the Bible. This may seem very obvious, however, since it is the most commonly used argument, I felt that demonstrating its weakness was probably worthwhile.
Edit: Additionally, I would point out that I am firmly in the first camp with regards to my usage of the term "unnatural" since I feel that it is the most meaningful.
Lastly out of these 3 definitions, none of them lead to a reasoned, logical conclusion that what is unnatural is wrong. However, some very clever people, realising that the final definition is neither reasoned nor logical, have decided that they are already not limited by such considerations and so are quite comfortable in declaring the immorality of homosexuality.