Perhaps the obfuscating issue here is whether one is using the
"alternativeWindowLook" or not.

Squeak 3.2 out-of-the box has alternativeWindowLook set on.  With
this kind of window-look, the saturated colors are confined to the
frame and scrollbars.

If you turn the alternativeWindowLook preference off (installing the
"brightSqueak" theme would be a good way to do this,) subsequent
launches of browsers, workspaces, etc., will yield the kind of
solid-color windows you may be wishing for.

OTOH if you wish to stay within the alternativeWindowLook regime but
just want to see a different neutral base color in the interiors of
the content panes, consider modifying method #paneColor: in
SystemWindow, where this is dealt with.  In the
alternativeWindowLook, the content panes are transparent, and the
color of the SystemWindow itself -- which is *not* the "paneColor",
shows through.