I don't really like to talk about rights of specific, narrow groups. I think that all people have the right to basically do as they please as long as they're not hurting anybody else. This includes the right to engage in discrimination based on any criteria, assuming no coercion or fraud is involved. This freedom does not extend to agents of the state acting in official capacity, as government should treat all people acting as specified above as equal under the law.
Regarding "defects" or "normal variations," I would say that transgender persons are neither; that is, while we appear to be rare, our accomplishments judged as a group seem to indicate that we are decidedly not "defective" (many good artists, musicians, scientists, etc.).
Regarding official (governmental) documentation, the best approaches would probably be an "other" option or making the question itself optional.
The government should have essentially nothing to do with marriage, and should not generally acknowledge it as distinct from any other contract between 2 or more consenting adults. Religious groups, employers, insurance companies, and other private actors (receiving no money from government/taxpayers) would decide what kinds of marriage they wish to recognize; I imagine that a small (but larger than now) number of distinct types would emerge with fairly broad acceptance.
Regarding protection from discrimination, everybody discriminates. It can be useful. To forbid people from discriminating based on selected factors does not change their beliefs; it just violates their rights, forces them to hide their discrimination, and stifles debate on the issue. If an individual or business discriminates based on invalid criteria (i.e. criteria that do not indicate criminality, unsuitability for a certain job, or anything else that might be considered negative), he/she/it/whatever will be harmed economically. In general, more open-minded people will be more successful, as they can hire the best employees regardless of race, religion, gender identity, etc. and do business with all willing customers.
You might not agree with me on all of this, which is to be expected. But I hope you will consider the importance of having an idea of rights that is as universal and durable as possible. Rights should not be applied only to certain people, nor should new rights usually have to be specified whenever a new race/religion/gender identity is created/discovered/officially recognized. I feel that giving the maximum possible liberty to all people is the best way to do this.