Found the answer via the scite-interest group: It's right in the docs: http://www.scintilla.org/SciTEDoc.html
To stop the output pane from automatically scrolling, set output.scroll to 0. To have the output pane scroll and return back to the line of the executed command, set output.scroll to 1. If you want the output pane to scroll and remain at the bottom after execution, set output.scroll to 2. The vertical scroll range is normally set so that maximum scroll position has the last line at the bottom of the view. Set end.at.last.line to 0 to allow scrolling one page below the last line.