tmux 1.7 and later include a speed limit view. This can help if the output you are working with is a normal "scrollable" output (many normal lines, and not (for example) a huge base64 encoded block).
Two options control this speed limit: c0-change-trigger and c0-change-interval . Basically, if tmux sees more than c0-change-trigger some C0 control characters (for example, backspace, linefeed, carriage return) in 1 millisecond, then it will postpone further updates to the panel in c0-change-interval milliseconds. By default, 250 such C0 characters in 1 millisecond stop drawing the panel for 100 milliseconds.