While the battle between the GDSs and their larger airline customers continues, I can't help but remember a similar time when SWA suddenly disappeared from Galileo (now Traveport) and agencies were scrambling for solutions. Fortunately, a few very bright programmers with access to the GDS and CompuServe were able to establish a link enabling agents to book SWA from any GDS workstation. GDSs would grumble and moan and threaten to pull agreements but I don't know that it ever happened and we sold a lot of SWADirect. At one point, it was even distributed by the GDSs to avoid agencies from switching to the competition. Fun times.
Now AA is potentially repeating history with much greater fanfare due to their size and impact upon the corporate market. Fortunately, most of the technology required to establish an elegant solution exists thru a combination of Farelogix (replaces CompuServe) and PASS Consulting with their GDS integration. The combination should promote AA at the right time and place. Online booking systems can simply link directly to Farelogix and be done with it (except for GetThere due to their Sabre ownership).
The bigger challenge for agencies is in data consolidation and down stream processes such as QA, ticketing, seat improvement, and backoffice reporting. When you book direct, there's no PNR, profile, segments, etc. Agency systems are dependent upon these items and without them, it becomes a mess that is either handled manually (expensive) or not at all. Without the records in the backoffice or flowing to ARC, peer to peer contracts are no longer as measureable. Automation for refunds and exchanges no longer work as well.
In the end, I'm confident these issues will be resolved just as they have with SWA. Technology solved the problem 10 years ago and will solve it again. This time around, the tool kit at least has the tools available to develop a viable solution.