If $g=\sum_k\beta_k\,1_{X_k}$ is simple,
$$
\Big\langle\Big(\int_\Omega g\,dE\Big)\xi,\xi\Big\rangle=\int_\Omega g\,dE_{\xi,\xi}=\sum_k\beta_k\,E_{\xi,\xi}(X_k)=\Big\langle\sum_k\beta_k\,E(X_k)\xi,\xi\Big\rangle.
$$
Since $g$ is measurable, then there exist simple functions $g_n$ such that $g_n\to g$ and $|g_n|^2\nearrow |g|^2$ (this is easily achievable by finding first simple functions that increase to $(\operatorname{Re}g)^+$, $(\operatorname{Re}g)^-$, $(\operatorname{Im}g)^+$, $(\operatorname{Im}g)^-$, respectively).
For any $\nu$ we have, using monotone convergence in each of the sixteen integrals coming from decomposing $g$ and $dE_{\xi,\nu}$ as a linear combinations of positive functions/measures,
$$
\langle \eta,\nu\rangle=\int_\Omega g\,dE_{\xi,\nu}=\lim_n\int_\Omega g_n\,dE_{\xi,\nu}=\lim_n\Big\langle\Big(\int_\Omega g_n\,dE\Big)\xi,\nu\Big\rangle
$$
So, writing $g_n=\sum_k\beta_{n,k}\,1_{X_{n,k}}$,
\begin{align}
E_{\eta,\eta}(A)
&=\langle E(A)\eta,\eta\rangle
=\Big\langle E(A)\Big(\int_\Omega g\,dE\Big)\xi,\eta\rangle\\[0.3cm]
&=\lim_n\Big\langle E(A)\Big(\int_\Omega g\,dE\Big)\xi,\Big(\int_\Omega g_n\,dE\Big)\xi\Big\rangle\\[0.3cm]
&=\lim_n\sum_k\overline{\beta_{n,k}}\Big\langle E(A)\Big(\int_\Omega g\,dE\Big)\xi,E(X_{n,k})\xi\Big\rangle\\[0.3cm]
&=\lim_n\sum_k\overline{\beta_{n,k}}\Big\langle \Big(\int_\Omega g\,dE\Big)\xi,E(A)E(X_{n,k})\xi\Big\rangle\\[0.3cm]
&=\lim_n\sum_k\overline{\beta_{n,k}}\Big\langle \Big(\int_\Omega g\,dE\Big)\xi,E(A\cap X_{n,k})\xi\Big\rangle\\[0.3cm]
&=\lim_n\lim_m\sum_k\sum_j\overline{\beta_{n,k}}\beta_{m,j}\Big\langle E(X_{m,j})\xi,E(A\cap X_{n,k})\xi\Big\rangle\\[0.3cm]
&=\lim_n\lim_m\sum_k\sum_j\overline{\beta_{n,k}}\beta_{m,j}\Big\langle E(A\cap X_{n,k})E(X_{m,j})\xi,\xi\Big\rangle\\[0.3cm]
&=\lim_n\lim_m\Big\langle \Big(\int_A \overline{g_n}g_m\,dE\Big)\xi,\xi\Big\rangle\\[0.3cm]
&=\lim_n\Big\langle \Big(\int_A \overline{g_n}g\,dE\Big)\xi,\xi\Big\rangle\\[0.3cm]
&=\Big\langle \Big(\int_A \overline{g}g\,dE\Big)\xi,\xi\Big\rangle\\[0.3cm]
&=\int_A|g|^2\,dE_{\xi,\xi}.
\end{align}