Well I am a general believer that Pioli was operating underneath Bill the whole time and that Bill was the one that had final say, with Pioli in more of an advising role. Most people in the media assume that it was Bill that was really calling the shots.
And from that same article on wiki
In 2005, he traded away top center Joe Thornton to the San Jose Sharks. The Bruins received players Brad Stuart, Marco Sturm and Wayne Primeau; Thornton went on with the San Jose Sharks to win the Hart Trophy as the league's most valuable player and the Art Ross Trophy as scoring champion. In trading Thornton, however, Boston freed up the necessary cap space to sign or re-sign free agents such as Zdeno Chára, Andrew Ference, Chuck Kobasew and Marco Sturm. He was replaced in his position as general manager by Peter Chiarelli.
So basically they had no cap room with the Thornton signing which is why they lost guys like Rolston, Knuble, and they had to trade away Thornton to gain cap space for other signings, which is what we may have had to do if they signed Seymour.