In a properly functioning society, with thoughtful, reasonable and educated statesmen governing the land and the people, with a balanced focus on that which benefits the nation versus what benefits individual groups, the tail should never wag the dog.
When a class/group/however you want to define it develops itself into a significant percentage of the population, there is a mechanism in place for them to acquire rights, protections and privileges, and that's proper, well and good. There's no logical fact-based reason why former slaves (primarily blacks) should not have been given rights protections and privileges following the abolition of slavery. As much a matter of it just being moral 'the right thing to do', a significant contributing factor in the equation had to be just how large a percentage of society they comprised. Society could not function with that high a percentage of it's members not being given equal rights.The same goes with homosexuals/bisexuals. Eventually they comprised a significant enough percentage of the population to gain access to rights, protections and privileges under the law.
Transgendered people are a very, very, very small minority in our current society...and there's plenty of research on both sides, indicating that it might be physiological issue, or that it might be a mental disorder, that plenty of reasonable people consider the jury still out on exactly what they are.
Due to the disproportionately small membership of the group, and the incomplete nature of the information about them, I don't think it's unreasonable at all to maintain the status quo until such time as the group grows larger, or more information-based conclusions can be drawn about them.
Either that, or we go back to having unisex, single use restrooms, and everyone gets to wait in line for each individual to do their business in private.