You could try to reposition the Button Bar using CSS (rather than the buttonBarPosition configuration option) but there may be unwanted knock-on side-effects (for example, when the browser window is resized and the gallery is redrawn) as Juicebox will know only of the configuration option settings and will not be aware of (or take into consideration) any changes to the default CSS rules in the 'theme.css' file. Also, depending on whether or not the Button Bar is positioned on the overlay, the visibility of the Button Bar may also have to be taken into consideration.
You could try using custom CSS (such as margins, padding or absolute positioning) on the .jb-bb-bar class but please note that such modifications are not officially supported and you may run into problems.