Yes, guest services at Downtown Disney still sells them.
Your other options are:
1.) purchase them online before you leave
pros - you have the pass before you leave
cons - voucher only/still need to go to guest services to activate, no savings in buying in advance
2.) purchase them at a
Disney Store - same pros and cons as #1
3.) purchase them at the Orlando airport Disney store (Disney's Earport - in the main terminal)
pros - eats time before you get to the baggage carousel to find it not moving, you get an ACTIVATED pass, not a voucher, one less thing to worry about before you actually get to Disney property
cons - if you pay with cash, you'll have to carry serious cash around airports, and airplanes - great risk of losing that much cash (if you pay by credit card, I really can't see any cons to buying them at the airport)
4.) purchase them at a Guest Services window (either at Downtown Disney, or any of the theme parks)
pros - you get an ACTIVATED pass
cons - you have to make a stop before you get to your hotel
Official Disney policy states that you need to have an activated pass when you check in in order to get the annual pass rate. That's the policy, but many report that they haven't had to show anything. Others report showing a voucher with no problems. Others report needing the activated pass, but showing the voucher, and stopping back at the front desk after the pass has been activated.
I too will be buying an Annual Pass for my trip in September. Assuming that AP rates come out for my period, I will probably purchase them at the airport. That seems the best option for me, because I don't want to take any chances with not being able to get the rate. Because you HAVE the rate, I'd say that's your best bet.
If I don't get an AP rate, I'll just go to the Guest Services window at the International Gateway (since I'll be at the Beach Club), and purchase them after checking in.
Have a FANTASTIC trip, and enjoy Pop Century!!!