Bukkit (the API that plugins link to) shouldn't be GPL. It is fully intended to have plugins link to it. They do on the github site. If that is their plan, then fair enough. However, they say that they don't intend (no legal weight) to force people to open source their code. It sounds like GPL is only temporary measure and they want to be more flexible. We don't know the discussions behind the scenes. There might be some legal issue with the fact that it is linking to a minecraft.