We don’t know how the schedule issues will work out in the long run, and it’s possible that “Game of Thrones” may diverge even more from “A Song of Ice and Fire” and start establishing its own canon. Of course, some characters and storylines are pretty much impossible to change at this point, but there are also plenty of opportunities for making the TV show look more unique and stand out on its own. However, some of those ideas will go against themes that have been established in the books already.
This will surely cause some controversy in the community though, so hopefully things won’t go that far. Or if they do, Martin would have to step forward and address the situation to let his followers know that he is on board with the whole project.
Whatever he is planning, we don’t expect to learn his intentions anytime soon. The writer is known for several things, his secretive nature being one of them. He rarely talks about his upcoming work, and when he does, his statements tend to bring up more questions than they answer.
So even if a scenario like the above is brewing up in the background, we don’t expect to find out about it until the last minute. Even then the news will probably come from the producers of “Game of Thrones” rather than Martin himself.