There have been no recent changes in the GAC (Guest Assistance Card) at WDW that I am aware of. There are several CMs in Guest Relations who have let us know about changes before, so if there were any changes, they would have said something.
It sounds like you got a CM who needed a little more pixie dust and I agree with Cheshire Figment that if a situation like that happens in the future, you should ask to speak to a supervisor.
Now, not knowing your exact situation, I can't say what occurred, but I can clarify some things about GACs and offer some educated guesses (I am not a WDW CM and I do not play one on TV, so do take these as best guesses).
First, the CMs do not have any medical background, so the CM in your case may not have recognized that Asperger syndrome is on the autism spectrum. Also, a lot of times when people do bring in doctor's letters, they might just say "Timmy has
x", or the letter may be several pages of specific medical information in medical language or just a short statement that says "let Timmy go on rides without waiting in line." (I'm not saying any of this was the case with your doctor letter).
None of those things are especially helpful to the CM.
The GAC is a tool to help the CMs know what sorts of accomidation are needed, so it's important that the CM issuing the GAC knows what the needs are. Two people with the same diagnosis might have very different needs, so the GAC is based on the needs, not the diagnosis. So, if someone comes in and says "I need a GAC because my child has x", but can't articulate any needs, they will not get a GAC. If they ask for something impossible, like front of the line access, they will not get a GAC. (I'm not saying this happened to you, especially since you mentioned in your post that your DS has some "issues" while in lines. I'm assuming either that you were able to explain the issues or the CM didn't let you get that far.)
Another thing that might have played into this is that at some times of the year, the waits in line are quite short and you don't really need a GAC. They used to tell people when they issued GACs that the GAC should only be used if the standby lines are more than 15-20 minutes.
This is normally a slow time and would have short waits, plus the Studio has a lot of attractions with Fastpass available (using Fastpass would definately shorten your wait in line to 10 minutes or less). It's possible the CM was told to convey that information to people who asked for GACs and sort of mis-stated it (with a little attitude).
No excuse for a rude CM. I hope you had a good day despite the bad start.