I don't remember No. 6 ever telling Baltar to betray Roslin and run for president nor do I recall Adama putting someone in command of the Pegasus

There have been a few times when cut or deleted scenes end up in the recap spots, you can see them online or on the DVDs. The Admiral has put both the Chief Eng. and a certain Major -- as you'll see at the end of this ep -- in command in uncut scenes. The only one he hasn't placed in command of the Peg. was her previous XO.