The one thing I don't buy in all of this is the anti-American accusations.
How many Americans were expelled due to UCI Pro Tour agreements the night before the Tour? None.
It's not a nationalistic problem in my mind. That's too convenient.
The leaks of the A sample are the bigger problem. You are correct that incompetence in this matter and others only erodes confidence in the sanctioning body's authority to rule in a fair manner.
That L'Equipe wants to sell more papers with accusations is a media tactic that has gone on much longer than professional sports have been around. That's just bad journalism and should not factor into the real case. It does affect the 'court of public opinion,' though, which is unfortunate.