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Quoting the manual:

Beamer-Color math text

This color is the parent of math text inlined and math text displayed. It is empty by default. See those colors for details.

Beamer-Color math text displayed

Color parents: math text

Like math text inlined, only for so-called “displayed” mathematical text. This is mathematical text between [ and ] or between $$ and $$ or inside environments like equation or align. The setup of this color is somewhat fragile, use at your own risk. The background is currently ignored.

So, you have to exploit:

\setbeamercolor{math text}{fg=pmsGreen}
\setbeamercolor{math text displayed}{fg=pmsGreen}

to have also equations in align colored (avoid using eqnarray, see eqnarray vs align).

An example:

\setbeamercolor{math text}{fg=pmsGreen}
\setbeamercolor{math text displayed}{fg=pmsGreen}



  1=2 \\
\item \only<2>{Contains essentially \textit{all} physical information of a given system} $A(\vec{r},\vec{r}^{'})=-\dfrac{1}{\pi}\im\Tr\int^{\mu}_{\curvearrowright} dz~\hat{A}~G(\vec{r},\vec{r}^{'};z)$

The result:

enter image description here