That line would have continued down Lafayette Avenue. On that Queens Bound G train at Bedford/Nostrand, Bedford Avenue exit would be at the back of the train.
This bellmouth that you're describing is it going into the Q and W line or would the Q and W line go into it? I ask because I have a set of BMT track maps prepared by David E Rogoff E.R.A. #1934. On Plate #4 dated 9/26/1966 there is a diagram for the BMT line from the Manhattan Bridge to 7th Avenue. After the train enters the portal there was a provision (bellmouth) for a turning track. From what I can gather, Trains going to Manhattan on the northside of the bridge would switch on to the turning track (I think it wouls be more like a set of tail tracks) where after the train changes ends, it would comeback on to the line on the Brooklyn Bound track on the southside of the bridge.