Is your thesis written in an RTL language? if it is and assumning, twoside option is used and bidi package is loaded, then bidi package takes care of this and puts margins in RTL mode in odd pages on LHS and in RTL mode in even pages, it puts margins on the RHS. Here is an example:
....
\usepackage{ptext}
\usepackage[demo]{graphicx}
\usepackage{xepersian}
\begin{document}
\ptext[1]
\begin{marginfigure}
\centering
\includegraphics[width=\textwidth]{demo}
\caption{این یک شکل است}
\end{marginfigure}
\ptext
\end{document}
and here is the output:

And the same example using bidi package and latin characters:
...
\usepackage{lipsum}
\usepackage[demo]{graphicx}
\usepackage[RTLdocument]{bidi}
\begin{document}
\lipsum[1]
\begin{marginfigure}
\centering
\includegraphics[width=\textwidth]{demo}
\caption{This is a figure}
\end{marginfigure}
\lipsum
\end{document}
\let\OldOddSideMargin\oddsidemargin \let\oddsidemargin\evensidemargin \let\evensidemargin\OldOddSideMargin. This works withbookclass, but I can't seem to get a two sided output withtufte-book. – Peter Grill Nov 18 '12 at 6:34\reversemarginpar. – Peter Grill Nov 18 '12 at 6:40tufte-bookclass so perhaps there is something special about that class that I am not aware of. It really would be helpful if you posted a fully compilable MWE including\documentclassand the appropriate packages that set up the problem. – Peter Grill Nov 18 '12 at 7:06