If the six runs in the first inning were the result of Pudge calling the wrong pitches, then why did they pull Marquis?
Because it wasn't (solely, anyway) the result of Pudge calling the wrong pitches, and you don't leave a pitcher in when he gives up 6 ER in 1/3 IP.
P.S. If Marquis didn't like where Pudge was setting up, guess what? He could make like Strasburg and shake him off. If you don't feel comfortable with a pitch, you don't have to make it! Marquis deserves at least as much blame as Pudge does if you think it was the pitch calling that led to his disastrous outing.