When assessing start/sit decisions based on the top pass defenses, one must remember teams that can't stop the run aften rank amongst the stingiest passing defenses. The structure of the NFL makes that so. There are just 60 minutes of clock and rushing the ball keeps the clock moving.
Amongst the legimate sit decisions to be made with this data, Tom Brady going against the Denver defense causes hesitition, but there is no one with the guts to sit Brady.
The one legitimate possible sit would be Atlanta Falcons' QB Matt Ryan. I'd hesitate sitting a Top 10 QB coming off a bye week, but the 49ers look like a legitmately good defensive club, and they are at home.