I also got stuck quite a well while understanding this proposition and the proof when I was new to commutative algebra.
Therefore I have written a detailed proof and tried to make it as readable and clear as possible:
Proof: We first clarify that by $\phi^n+a_1 \phi^{n-1}+\cdots+a_n=0$ the author actually means
\begin{equation*}
\phi^n(x)+a_1 \phi^{n-1}(x)+\cdots+a_nx=0,\, x\in M.
\end{equation*}
Let us continue with the following equation (where I substituted $a_{ij}\gets -a_{ij}$ for convenience):
\begin{align*}
(\phi(x_1)+a_{11}x_1)&+a_{12}x_2&+\cdots&+a_{1n}x_n&=0.\\
a_{21}x_1&+(\phi(x_2)+a_{22}x_2)&+\cdots&+a_{2n}x_n&=0.\\
\cdots\\
a_{n1}x_1&+a_{n2}x_2&+\cdots&+(\phi(x_n)+a_{nn}x_n)&=0.
\end{align*}
Given $a\in A$, we define $l_a:M\to M, m\mapsto am$. We note that $l_a$ is actually an $A$-module endomorphism of $M$.
If we set
\begin{equation*}
\psi_{ij}=\delta_{ij}\phi+l_{a_{ij}}=\begin{cases}
l_{a_{ij}}, &i\ne j\\ \phi+l_{a_{ij}}, &i=j
\end{cases},
\end{equation*}
then $(\psi_{ij})$ are also endomorphisms of $M$, and by hypothesis
\begin{equation}
\sum_{i=1}^n \psi_{ki}(x_i)=0,\, 1\le k\le n. \tag{$\star$}
\end{equation}
Note that $\psi_{ij}\in \text{End}_R(M)$ and $M$ naturally has an $\text{End}_R(M)$-module structure
(the multiplication of the ring $\text{End}_R(M)$ is composition),
the scalar multiplication of which is $(\psi,m)\mapsto \psi(m)$.
We may abuse the notation and write this scalar multiplication as $\psi m$.
Then ($\star$) becomes \begin{equation}
\sum_{i=1}^n \psi_{ki}x_i=0,\, 1\le k\le n. \tag{$\star\star$}
\end{equation}
Note that $\text{End}_R(M)$ is not necessarily a commutative ring, but $\psi_{ij}$s commute:
we just do a casework and verify $\psi_{i_1j_1}\psi_{i_2j_2}=\psi_{i_2j_2}\psi_{i_1j_1}$ when
\begin{equation*}
\begin{cases}
i_1=j_1,\, i_2\ne j_2\\
i_1\ne j_1,\, i_2\ne j_2\\
i_1=j_1,\, i_2=j_2
\end{cases}.
\end{equation*}
Therefore the subring $S$ generated by $\psi_{ij}$s (and $1_{\text{End}_R(M)}$)
\begin{equation*}
S=\{ \sum_{l=1}^N \xi_{l,1}\cdots \xi_{l,{k_l}}: \xi_{p,q}\in \{\psi_{ij}\}\cup {1_{\text{End}_R(M)}}, N,k_1,\cdots,k_N\in\mathbb{Z}_+ \}\cup\{0_{\text{End}_R(M)}\}
\end{equation*}
is commutative, and $M$ is an $S-$module, and $(\star\star)$ can be viewed as an equation on $S-$module action.
Finally, that $\det(\psi_{ij})=0_{\text{End}_R(M)}$ can be inferred from the following lemma
(applied to $S-$module $M$) and that $M=\sum_{i=1}^n Ax_i$:
Lemma: Let $A$ be a commutative ring and $M$ an $A$-module.
If $(a_{ij})_{1\le i,j\le n}\in A$ and $\sum_{i=1}^n a_{li}m_i=0$ for each $1\le l\le n$,
then $\det(a_{ij})_{n\times n} m_l=0$ for each $1\le l\le n$.
Proof of the Lemma: Set $D=\det(a_{ij})_{n\times n}$. We only prove $Dm_1=0$, proof of the other equalities being similar.
In fact, let $c_{ij}$ denote the cofactor of $a_{ij}$ in $\det(a_{ij})_{n\times n}$.
Then \begin{equation*}
0=\sum_{l=1}^n c_{1l} \left( \sum_{i=1}^n a_{li}m_i\right) .
\end{equation*}
Let us study the coefficient of $m_i$s in the above equation:
the coefficient of $m_1$ is $\sum_{l=1}^n c_{1l} a_{l1}=D$,
while for $m_i$ ($i\ne 1$), its coefficient is $\sum_{l=1}^n c_{1l} a_{li}$, which is
the determinant of a matrix the first and $i-$th column of which are both $(a_{1i},a_{2i},\cdots,a_{ni})^T$,
and is therefore $0$, i.e. $Dm_1=0$ as desired. $\square$
Recall that $\psi_{ij}=\delta_{ij}\phi+l_{a_{ij}}$. Clearly $\det(\psi_{ij})=0_{\text{End}_R(M)}$ implies the long-desired existence of an equaton of the form
\begin{equation*}
\phi^n(x)+a_1 \phi^{n-1}(x)+\cdots+a_nx=0.\, \square
\end{equation*}