Carlson and McDonnell said that they had literally 48 hours to write the entire script before shooting began and it clearly shows in a number of spots. Charybdis could not possibly have planned ahead of time to frame Starbuck, because he couldn't have anticipated Starbuck being thrown out of the game and thus being in position for him to become the fall guy. Clearly, Charybdis must have had some alternate plan initially that involved killing Charybdis.
On the plus side, the mere existence of Charybdis and his being referenced as "Baltar's pilot" clears up the mystery of how Baltar got off the Atlantia before the attack began in Saga. Clearly, Charybdis after doing the sabotage work, must have been waiting in a shuttle aboard the Atlantia for Baltar to board at the right opportunity.
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