John,
The only problem that I think the side by side layout will have is when a thread grows deep enough. Either the indentation for a tree will be so small as to be nearly imperceptible or it won't take a very deep nesting to overrun the width of the frame. Perhaps you could try incorporating your ideas into the over under frames with what you currently have on top being moved to the left.
The thing is that right now we have approx 2/3rds of the screen height for the message body and 1/3 for teh message tree. 3/4 of the width is available for the message body and the tree. Your example is givin us more height for the tree but less width (and the tree needs the width more than the height).
The message body doesn;t make much difference whether it gets height or width as either one allows more text (one by more lines and the other by more columns).
So, I guess I'm saying that I think the message tree needs to be a wide area. That would mean it needs to be above or below other frames and be full width.