$\newcommand{\De}{\Delta}$The answer is: not in general.
Indeed, suppose the contrary. Let
\begin{equation}
A:=\begin{pmatrix}
0&1/2\\
1/2&0
\end{pmatrix},
\end{equation}
so that
\begin{equation}
(\De_A f)(s,t)=\frac{\partial^2 f(s,t)}{\partial s\,\partial t}=f^{(1,1)}(s,t).
\end{equation}
Let
\begin{equation}
O:=\begin{pmatrix}
0&-1\\
1&0
\end{pmatrix}
\end{equation}
and
\begin{equation}
g:=\varphi_O,
\end{equation}
so that
\begin{equation}
(Gf)(s,t):=e^{g(s,t)}f(-t,s),
\end{equation}
and the difference between the right-hand side and left-hand side of the equality in question
divided by $e^{g(s,t)}$ is
\begin{equation}
\begin{aligned}
d_f(s,t)&:=\frac{(G(\De_A f))(s,t)-(\De_A(Gf))(s,t)}{e^{g(s,t)}} \\
&=\frac{e^{g(s,t)}f^{(1,1)}(-t,s)
-\dfrac{\partial^2 f(s,t)}{\partial s\,\partial t}
\big(e^{g(s,t)}f(-t,s)\big)}{e^{g(s,t)}} \\
&=-f^{(0,1)}(-t,s) g^{(0,1)}(s,t)+f^{(1,0)}(-t,s) g^{(1,0)}(s,t)
+2 f^{(1,1)}(-t,s) \\
&-f(-t,s)
\left(g^{(0,1)}(s,t) g^{(1,0)}(s,t)+g^{(1,1)}(s,t)\right)=0
\end{aligned}
\end{equation}
for all $f\in C^1$ and all real $s,t$.
Letting now $f_1(s,t):=s$, $f_2(s,t):=t$, and $f_4(s,t):=t^2$, we get
\begin{equation}
0=s d_{f_2}(s,t)-d_{f_4}(s,t)=s g^{(0,1)}(s,t),
\end{equation}
so that $g^{(0,1)}=0$ and hence $g^{(1,1)}=0$, which implies $0=d_{f_1}=g^{(1,0)}$.
So, $g$ is a constant, and hence
$0=d_f(s,t)=2f^{(1,1)}(-t,s)$ for all $f\in C^1$ and all real $s,t$, which is absurd. $\quad\Box$