Currently, beamer inserts the ToC and Navigation entries to match the mandatory sectioning command. You'll have to patch each sectional unit separately to "fix" this:

\documentclass{beamer}
\usepackage{etoolbox}
\makeatletter
% Insert [short title] for \section in ToC
\patchcmd{\beamer@section}{{#2}{\the\c@page}}{{#1}{\the\c@page}}{}{}
% Insert [short title] for \section in Navigation
\patchcmd{\beamer@section}{{\the\c@section}{\secname}}{{\the\c@section}{#1}}{}{}
% Insert [short title] for \subsection in ToC
\patchcmd{\beamer@subsection}{{#2}{\the\c@page}}{{#1}{\the\c@page}}{}{}
% Insert [short title] for \subsection in Navigation
\patchcmd{\beamer@subsection}{{\the\c@subsection}{#2}}{{\the\c@subsection}{#1}}{}{}
\makeatother
\begin{document}
\begin{frame}
\tableofcontents
\end{frame}
\section[short section]{long section}
\subsection[short subsection]{long subsection}
\frame{}
\end{document}
\beamer@section[#1]{#2} and \beamer@subsection[#1]{#2} act very much like the regular \section[#1]{#2} and \subsection[#1]{#2}, writing #2 to the .toc and .nav auxiliary files. The above \patchcmd{<cmd>}{<search>}{<replace>}{<success>}{<failure>} switches the mandatory one for the optional one when writing to the auxiliaries.
\insertsectionbut the short form in the TOC – samcarter_is_at_topanswers.xyz Sep 25 '14 at 16:30