[guided]The phase has no stationary point in the $\xi$ variable when $x \ne y$, because its $\xi$-gradient is the nonzero vector $x-y$. This is the reason the kernel becomes smooth away from the diagonal. We turn that observation into an estimate by using an integration-by-parts operator that reproduces the exponential.
For $(x,y)\in \operatorname{supp}\eta$, define
\begin{align*}
L_{x,y}: C^\infty(\mathbb{R}^n_\xi) &\to C^\infty(\mathbb{R}^n_\xi)
\end{align*}
by
\begin{align*}
L_{x,y}q(\xi)=\frac{1}{i|x-y|^2}\sum_{j=1}^n (x_j-y_j)\frac{\partial q}{\partial \xi_j}(\xi).
\end{align*}
This operator is chosen so that applying it to the exponential returns the exponential itself:
\begin{align*}
L_{x,y}\left(e^{i(x-y)\cdot \xi}\right)=\frac{1}{i|x-y|^2}\sum_{j=1}^n (x_j-y_j)i(x_j-y_j)e^{i(x-y)\cdot \xi}=e^{i(x-y)\cdot \xi}.
\end{align*}
Because $\operatorname{supp}\eta$ is disjoint from the diagonal, the denominator $|x-y|^2$ is bounded below there by a positive constant. Thus the coefficients of $L_{x,y}$ and of its formal transpose $L_{x,y}^t$ are smooth and bounded on compact subsets of $\operatorname{supp}\eta$.
Now integrate by parts $N$ times in the $\xi$ variable. No boundary term appears in the oscillatory-integral interpretation, equivalently after inserting a compactly supported cutoff in $\xi$ and passing to the oscillatory limit. Since $L_{x,y}$ fixes the exponential, we obtain
\begin{align*}
\operatorname{Os}\!\int_{\mathbb{R}^n} e^{i(x-y)\cdot \xi}\eta(x,y)a(x,\xi)\,d\mathcal{L}^n(\xi)
\end{align*}
equal to
\begin{align*}
\int_{\mathbb{R}^n} e^{i(x-y)\cdot \xi}(L_{x,y}^t)^N\left(\eta(x,y)a(x,\xi)\right)\,d\mathcal{L}^n(\xi).
\end{align*}
Each application of $L_{x,y}^t$ differentiates the amplitude once in $\xi$ and multiplies by a smooth coefficient depending on $(x,y)$. Since $a \in S^m_{1,0}(U \times \mathbb{R}^n)$, differentiating once in $\xi$ lowers the order by one. Therefore $(L_{x,y}^t)^N(\eta a)$ has order $m-N$ in $\xi$. Choose $N$ so that $m-N<-n$. Then the bound by a constant multiple of $(1+|\xi|)^{m-N}$ is integrable over $\mathbb{R}^n$ with respect to $\mathcal{L}^n$, so the resulting integral is absolutely convergent and locally uniform in $(x,y)$.[/guided]