Stephen wasn't one of the Twelve, and we don't even know if he claimed to have seen Jesus after his resurrection. So is the stoning of Stephen irrelevant to the trilemma argument for the Twelve? Nope. If a leader of your community was lynched by a mob for preaching a sermon, and if more and more people from your community were then dragged out to jail (as happened in the persecution from Saul of Tarsus), that would mean that it would take courage to go on saying what that person was killed for saying. And the Apostles stayed in Jerusalem during the persecution from Saul. Later, James the son of Zebedee (one of the Twelve) was killed by Herod Agrippa I.

Acts has lot to say about the courage of the Twelve under persecution. Acts strongly supports the claim that they were attesting to Jesus' resurrection at the risk of their lives.