i don't think its unreasonable to suggest there was some amount of collusion/cooperation between law enforcement and MLB in this instance.
the timing of the indictment is league-friendly. after barry bonds parted ways with the giants. after the world series and season was over. the last thing MLB would've wanted was this shit to come down and detract from the actual game.
as far as a conspiracy by bud selig to "get" barry bonds, i don't buy it.
bud selig didn't instruct barry bonds to be non-responsive during testimony. if you read the transcript, barry bonds was being elusive in his answers, and to law enforcement, that is a prime indicator of deception.