$\newcommand{\ga}{\gamma}\newcommand{\Ga}{\Gamma}\newcommand{\al}{\alpha}\newcommand{\p}{\partial}\newcommand{\de}{\delta}$Without loss of generality (wlog), $\ell$ is the uniform probability distribution over $E$ and hence
$\sum_{i=1}^N\al_i=1$. Here it is assumed that the interior $E^\circ$ of $E$ is nonempty.
Let $\Ga$ be the set of all probability distributions $\ga$ over $E\times E$ such that for some $(x_1,\dots,x_N)\in E^N$ the marginals of $\ga$ are $\sum_{i\in[N]}\al_i\de_{x_i}$ and $\ell$, where
$[N]:=\{1,\dots,N\}$. Informally, $\ga(X\times A)$ is the mass transported from a set $X$ to a set $A$ under the plan $\ga$.
Let $\ga^*\in\Ga$ with marginals $\sum_{i\in[N]}\al_i\de_{x_i^*}$ and $\ell$ be an optimal transportation plan in the sense that
\begin{equation*}
C(\ga):=\int_E|x-y|^2\,\ga(dx\times dy)\ge C(\ga^*)
\end{equation*}
for all $\ga\in\Ga$, where $|\cdot|$ is the Euclidean norm.
Claim: $x_i^*\in E^\circ$ for all $i\in[N]$.
Proof: Suppose the contrary. Then wlog $x_1^*\in\p E$. So, wlog $x_1^*=(0,0)$ and $(s,t)\in E$ implies $s\le0$ -- that is, the first coordinate of any point in $E$ is $\le0$. Let
\begin{equation*}
\ga_i^*(A):=\ga^*(\{x_i^*\}\times A)
\end{equation*}
for all Borel subsets $A$ of $E$.
To simplify writing, suppose that the $x_i^*$'s are pairwise distinct.
Then
\begin{equation*}
C(\ga^*)=\sum_{i\in[N]}\int_E|x_i^*-y|^2\,\ga_i^*(dy).
\end{equation*}
(Otherwise, first rewrite $\sum_{i\in[N]}\al_i\de_{x_i}$ as $\sum_{i\in[n]}\beta_j\de_{z_j}$ with pairwise distinct $z_j$'s and appropriate $n$ and $\beta_j$'s.)
Also, $\ga_1^*(\p E)\le\ga^*(\{x_1^*,\dots,x_N^*\}\times\p E)=\ell(\p E)=0$ and hence $$\ga_1^*(E^\circ)=\ga_1^*(E)-\ga_1^*(\p E)=\ga_1^*(E)=\al_1>0.$$
Therefore and because the first coordinate of any point in $E$ is $\le0$, the first coordinate of the barycenter $\bar x_1^*$ of the measure $\ga_1^*$ is $<0$. So, $\bar x_1^*\ne(0,0)=x_1^*$. Also, $\bar x_1^*\in E$, since $E$ is convex.
Moreover, it is easy to see (say, by differentiation) that $\bar x_1^*$ is the unique minimizer of $\int_E|x-y|^2\,\ga_1^*(dy)$ over $x\in E$.
It follows that
\begin{equation*}
C(\bar\ga^*)<C(\ga^*), \tag{3}\label{3}
\end{equation*}
where
$\bar\ga^*\in\Ga$ is defined by the conditions
\begin{equation*}
\bar\ga^*(\{x_i^*\}\times A)=\ga^*(\{x_i^*\}\times A) \quad\text{if }i\in\{2,\dots,N\},
\end{equation*}
\begin{equation*}
\bar\ga^*(\{\bar x_1^*\}\times A)=\ga^*(\{x_1^*\}\times A)
\end{equation*}
for all Borel $A\subseteq E$.
Inequality \eqref{3} contradicts the optimality of $\ga^*$. $\quad\Box$