The allowance of Transgender people into the Military is currently being viewed and associated directly with the recent changes in laws and regulations allowing Gay/Lesbians serve openly and marry significant partners.
Transgender is not the same as Gay or Lesbian. These individuals identify with the opposite gender that they are biologically and seek to change their physiology to match their mindset. Many utilize surgery and hormone therapy to modify themselves to suit their desires. This course of action heavily impacts their medical and psychological health.
Having a person who is of a different gender then they are according to their DNA creates a greater chance of dangerous situations for them in a Military capacity. Another question would be how to treat them, male or female?