My common sense tells me that it is natural for me to be gay but it is not natural for a person to want to amputate a limb or two. But philosophically and morally who am I to tell them there is something wrong with them?
Our moral imperative is to prevent people from hurting themselves because of psychological issues. Amputations brush up against that moral imperative. Being gay does not. You are harming no one, and are in fact improving your life by being involved in relationships that enrich your life.
The other problem you seem to be having is that you are confusing two different usages of the word "natural". There is natural as in how nature operates, and also natural as in how something usually operates to the benefit of the body. Those two are not the same.