As simple functions with "rectangles" as "steps" are dense in $L^2(\Omega^2)$, there is a sequence $k_n \in L^2(\Omega^2)$ of functions of the form
\[
k_n(x,y) = \sum_{i=1}^{N_n} a_{i}\chi_{A^n_i}(x)\chi_{B^n_i}(y)
\]
where $A^n_i$, $B^n_j \subseteq \Omega$ are of finite measure, such that $k_n \to k$ in $L^2(\Omega^2)$.
Define $K_n$ as $K$, but with $k$ replaced by $k_n$. Then we have for $f \in L^2(\Omega)$ and $x \in \Omega$
\begin{align*}
(K_nf)(x) &= \int_\Omega k_n(x,y)f(y)\,d\mu(y)\\
&= \sum_{i=1}^{N_n}a_i\chi_{A^n_i}(x)\int_\Omega \chi_{B^n_i}\, d\mu\\
&= \sum_{i=1}^{N_n}a_i \mu(B^n_i) \cdot \chi_{A^n_i}(x)
\end{align*}
That is $K_n f \in \operatorname{span}\{\chi_{A^n_i} \mid 1 \le i \le N_n\}$. As $f$ was arbitrary, $\dim\operatorname{ran} K_n \le N_n$, so $K_n$ is compact. Also we have
\begin{align*}
\|K_n f - K f\| &\le \left( \int_\Omega\left|\int_\Omega (k_n - k)(x,y)f(y)\,dy\right|^2\, dx\right)^{1/2}\\
&\le \left(\int_\Omega \int_\Omega |(k_n-k)(x,y)|^2\, dy\cdot \|f\|^2\, dx\right)^{1/2}\\
&\le \|k_n - k\|_{L^2(\Omega)^2}\|f\|_{L^2(\Omega)}
\end{align*}
So $\|K_n - K\| \le \|k_n - k\| \to 0$ and $K$ is compact as a limit of compact operators.
First we show that $(\phi_{ij})$ is orthonormal. We have for $i,j,k,l \in I$
that $\def\skp#1{\left\langle#1\right\rangle}$
\begin{align*}
\skp{\phi_{ij}, \phi_{kl}} &= \int_{\Omega^2} e_j(x)\overline{e_i(y)}\overline{e_l(x)\overline{e_k(y)}} \, d\mu^2(x,y)\\
&= \int_\Omega e_j\overline{e_l}\, d\mu \cdot \int_\Omega \overline{e_i}e_k\, d\mu\\
&= \skp{e_j,e_l}\cdot \skp{e_i, e_k}\\
&= \delta_{jl}\delta_{ik}
\end{align*}
Moreover
\begin{align*}
\skp{k, \phi_{ij}} &= \int_{\Omega^2} k(x,y)\overline{e_j(x)\overline{e_i}(y)}\, d\mu^2(x,y)\\
&= \int_\Omega \left(\int_\Omega k(x,y)e_i(y)\,d\mu(y)\right) \overline{e_j(x)}\, dx\\
&= \int_\Omega Ke_i(x)\overline{e_j(x)}\, d\mu\\
&=\skp{Ke_i, e_j}
\end{align*}