I can see why this is done. I personaly have no problem with gays in the military, or in general for that matter, it's not like they have not been there since day one. The main concern is "unit cohesion". There's a lot of this talked about, but unless you've been there, been a part of it, it's hard to wrap your head around.
Sports teams, cops, firefighters, military, etc... These are all groups that can and do become closer to you than your own family. People who, in many cases, you would gladly lay down your life for them, knowing they would jump at the chance to do the same for you. It's a very deep, visceral thing.
The open minded attitude is not yet wide spread enough to allow that lifestyle into the "group". It's pretty sad, really. However, that's the cold truth.
In "normal life" there are cases of shunning, and finger pointing, etc.. In the military, despite the doctrine of "everyone is green, just like you" gays are downright persecuted. Hate to put it bluntly, but look at the vast demographic makeup of the military. Not that many activists and PhD's running around with Sergeant stripes on, if you know what I mean. That is what the article means by the fact the military is "20 years behind society". I think that's a generous estimate.
Units like linguists, intel, Spec Ops, etc.. are very, very small worlds. You can be stationed with the same group of 100 or so people (with variations) for a full 20 year career. The camaraderie is palpable. (Just ask my wife who was on the outside, looking in)
Unfortunately, there are going to be some areas of life where gays may never be "accepted". As wrong as this is, it's true.
It does not matter how "good" you are. I'm a prime example. I'm straight, married, and was in the top 2% of Intel/Linguists in the US Army. I get hurt, (blow out 2 disks in my lower back), and rather than try and re-hab me, or give me time to heal, Uncle Sam just says "well, son, your broke. It's been fun, have a nice time and don't let the door hit you on the way out."
Keep in mind that Intel is not an overly physically demanding field, depending on the unit to which you are assigned. That's just the mentality. If you are "different" (i.e.. hurt/rich/Muslim/gay/etc...) you don't "belong". The military, as a whole, is perhaps the single most homogeneous group of individuals on the planet. If you don't "fit in", it is not a fun place.
The mantra is "everyone is green, just like you", the practice is different.