Let $T\colon (x,y)\mapsto (x-y,y)$. Then
$$E[g(B_t,B_s)]=E[h(B_t-B_s,B_s)],$$
where $h(T(x,y))=h(x-y,y)=g(x,y)$. This gives, using independence of the increments of Brownian motion, and a density of $(B_t-B_s,B_s)$, and a substitution,
\begin{align}
E[g(B_t,B_s)]&=\int_{\Bbb R^2}h(u,v)\frac 1{\sqrt{2\pi(t-s)}\sigma}\frac 1{\sqrt{2\pi s}\sigma}\exp\left(-\frac 1{2\sqrt{\sigma}}\left(\frac{u^2}{\sqrt{t-s}}+\frac{v^2}{\sqrt s}\right)\right)dudv\\
&=\frac 1{2\pi\sigma^2}\int_{\Bbb R^2}g(x_1,x_2)\exp\left(-\frac 1{2\sqrt{\sigma}}\left(\frac{(x_1-x_2)^2}{\sqrt{t-s}}+\frac{x_2^2}{\sqrt s}\right)\right)dx_1dx_2.
\end{align}
We can generalize this: if $t_1<\dots