Since you don't seem interested in the location list, you could change the location counter to section and define a glossary style that checks if the current section is in the location list. You'll probably want to neaten the glossary, but here's an example:
\documentclass{article}
\usepackage{datatool-base}
\usepackage[counter=section,xindy]{glossaries}
\GlsSetXdyMinRangeLength{0}
\makeglossaries
\newglossaryentry{E}{name={\ensuremath{E}},
description={energy}}
\newglossaryentry{m}{name={\ensuremath{m}},
description={mass}}
\newglossaryentry{c}{name={\ensuremath{c}},
description={speed of light}}
\newglossaryentry{v}{name={\ensuremath{v}},
description=velocity}
\newglossarystyle{mystyle}%
{%
\glossarystyle{list}%
\renewcommand*{\glossaryentrynumbers}[1]{\striprelax##1\endstriprelax}%
\renewcommand*{\glsXsectionXglsnumberformat}[2]{##2}%
\renewcommand*{\delimR}{,}%
\renewcommand*{\glossaryentryfield}[5]{%
\edef\doifinlocation{\noexpand\ifinlocation{\thesection}{##5}}%
\doifinlocation
{%
\item ##2 ##3%
}%
}%
}
% \ifinlocation{number}{location list}{body}
\newcommand{\ifinlocation}[3]{%
\DTLifinlist{#1}{#2}{#3}{}%
}
\def\striprelax\relax#1\endstriprelax{#1}
\glossarystyle{mystyle}
\begin{document}
\section{Sample Section}
\printglossary
\begin{equation}
\gls{E} = \gls{m}\cdot \gls{c}^2
\end{equation}
\section{Another Section}
\printglossary
\begin{equation}
\gls{E} = \frac{\gls{m}\gls{v}^2}{2}
\end{equation}
\end{document}
Note that this uses xindy rather than makeindex to suppress the range formation, which makes it easier to test if the current section is in the list.
The result looks like:
