If this is the way AK has been run all along, greasing palms and several layers of connections under the table, then what Nik said about the paybacks/bidding war seems most likely.
Regarding Nike's role/relationship with AK, it seems far more likely that the business giant Nike would be far more interested in having its own sponsored athletes on the team, like another poster said, rather than taking the stance of the old, idealistic, anti-AAU/anti-establishment basement operation (the "grass-roots" Nike, which may well myth anyway...Nike and Pre being synonymous doesn't necessarily mean there was a common goal between them.)
The articles that the Ethiopian journalist provided shows that the Ethiopian Federation does exercise tight control over its athletes, and this is something that AK may be trying to emulate. But if these "rules" that caused these athletes to be dropped are made up after the fact, or to fish for some paybacks, then really this is a thinly-disguised crime, and the higher-ups at AK are criminals.
The boycott idea would falter because there must be dozens of desperate souls who could be right at the cusp of greatness, and who might well do anything to make a breakthrough at the world-level.
I wonder if someone like Paul Tergat spoke up, as he has before, or other great names from the past, whether that would make a difference. But even in Ethiopia, the greats of today such as Haile and Bekele never comment publicly on wrongs of the past, like the injustice that happened to Mamo Wolde and his family (There was an amazing article written by Kenny Moore about this, recounting what happened during the Munich marathon, and prior to and after the 1996 Olympics - I wish I had that link...) I guess it is difficult and a little unfair to expect that even those with the accomplishments, reputation and position to be listened to have the obligation to speak out - that doesn't happen very often anyway.
I hope these athletes get their shot, somehow. But the duo at AK are a pair of sad, petty criminals. It is difficult to see how the IAAF can sanction AK - maybe they should be more like FIFA, and refuse to recognize AK as legitimate - probably also a pipe-dream since they are fine with USATF.