Here is a solution that patches an auxiliary macro in \frametitle, adding code that adds a table-of-contents line as if it were a subsection:
\documentclass{beamer}
\AtBeginSection{\frame{\tableofcontents[currentsection]}}
\usepackage{bookmark}
\usepackage{etoolbox}
\makeatletter
\apptocmd{\beamer@@frametitle}{
% keep this line to add the frame title to the TOC at the "subsection level"
\addtocontents{toc}{\protect\beamer@subsectionintoc{\the\c@section}{0}{#1}{\the\c@page}{\the\c@part}%
{\the\beamer@tocsectionnumber}}%
% keep this line to add a bookmark that shows up in the PDF TOC at the subsection level
\bookmark[page=\the\c@page,level=3]{#1}
}%
{\message{** patching of \string\beamer@@frametitle succeeded **}}%
{\message{** patching of \string\beamer@@frametitle failed **}}%
\makeatother
\begin{document}
\section{First Section}
\begin{frame}{First frame}\end{frame}
\begin{frame}{Second frame}\end{frame}
\section{Second Section}
\begin{frame}{Third Frame}\end{frame}
\begin{frame}{Fourth frame}\end{frame}
\end{document}
I had to dig around in beamerbasesection.sty to figure that out. But it seems to work.
EDIT. I put in the bookmarking this time. Rather than delete the code which does something you didn't ask for, I left it for you to comment out.