Issue of Transgender legal status

Ok, firstly i have no problem with transgender people. I feel that a person has to right to be happy in their own skin. 

My problem comes from the point of view of my own field of interest, Forensic Detection. 

Let me paint a picture:

A murder seen is discovered and some hair/skin cells are the only evidence that was able to be collected. Upon analysis it is determined that the suspect is a caucasian male. The suspect DNA is passed through tall the available databases and again no hit. The only suspects are a young black male and a middle age woman. 

So who could it be. 

My problem is that despite the fact the woman is now officially and legally a woman, she was born a man. her DNA still shows that she is a man! 

Now i do feel that all transgender persons should have status, but for official documents it should say that the person is Transgender. i know this seems harsh but if it helps to save lives, or help speed up the legal system then yes, i believe it would be a positive step. 

When i say Official documents, i mean official ID, all government records etc. the persons own personal ID, College etc, should state her sex as Female.

I'm open to comments or criticisms on this point.

Thoughts on this?