As I see it the issue is, as it often is, that society and science have different perceptions on what the term "mental disorder" means.
Society seems to see it as a negative thing that means there is something wrong with the person and we should be spending resources on trying to find a cure so we can fix them and they can become normal again. The "progressive" crowd generally doesn't like implying that there is ever anything wrong with you, and so they don't like the classification.
Science on the other hand really just defines it as any mental condition which influences thinking and/or behaviour, not counting temporary changes that come as a result of consumption of things like alcohol(sorry, but being drunk isn't a disorder =P). Although addiction to substances do qualify as a disorder.
The thing that a lot of people need to understand is that the scientific community usually defines things based on what causes them and how they affect you. Transgenderism can be classified as a mental disorder because the cause and effects fall under that category. It is something that is mental, and it is most certainly something that affects thinking and behaviour.
From a biological standpoint cis/heterosexuality is considered what is normal because that's how our species reproduces and that is how the vast majority of humans are(even if you count the highest 12% estimate). You can try as much as you'd like, but two men having sex can't produce a child.
I would argue that we need to drop the stigma about mental illness/disorders. When science calls something a mental disorder, it's not saying that you need to be "cured into being cis". Society is the one thinking that.