There must be a director, or some other person who can act as stage manager at every performance. The audience should not be told what that time limit is. Have pre-arranged signals with characters so that the facilitator knows when to intervene. Direct questions towards the audience, not the actors. Audience should not give notes.
Silence is ok.
The audience still can not critique acting. This part of discussion should last a max of 15 minutes before we break out altogether. Both in and out of character, actors can choose to pass on any question they feel that they cannot answer. Today was work on the assault portion of the scene. It doesn't get easier the longer you do it, but it does when you know the person you're playing against - there's a comfort level that's already been established.