Former Cosatu general secretary Zwelinzima Vavi and EFF leader Julius Malema are plotting to overthr.
Pirates chairman Irvin Khoza revealed that Boa Morte was frustrated at not being picked by coach Augusto Palacios following his recovery from injury.
"He is not missing from training. We had a conversation with him and he asked if he could be released from his contract because he is not being picked for the team by the coach," said Khoza. "We accepted his request and he has now gone back home."
Boa Morte, 34, was convinced by his friend and teammate Benni McCarthy to join Pirates this season, but only made three appearances for the Buccaneers in the Absa Premiership since signing.
Meanwhile, the Pirates chairman confirmed the search for a new coach for the defending champions and log leaders has intensified.
The Buccaneers are looking to fill the gap left by Julio Leal, who resigned in April, leaving Palacios to take over until the rest of the season.
"Our concentration is on the last game of the season against Golden Arrows (on Saturday) and after that we will then make the necessary announcements. We don't want to pile pressure on our players and the current technical team when we have a chance to make history by winning a second successive treble," said Khoza.