President Obama has no idea how to be Commander in Chief. What a commander does is call in the joint chiefs.
"Gay men and Lesbian women may now serve in the Armed Forces. You will no more task them with the sodomy portions of the UCMJ than you currently task your heterosexual troops who get or give oral and other kinds of sex. If any of you cannot follow this order, I will accept your resignations as soon as this meeting is over."
That is what a commander does. He doesn't waffle about what his orders are.
The only part of the military that is not ready for this move is the part in charge, and the part that is so right wing Taliban that they would perfer persecution to peace.