[guided]The only subtle point is that atoms of measure zero can make $I_\mu(\alpha)$ take the value $+\infty$, because we use the convention $-\log 0=+\infty$. These atoms should not affect the integral, but we must justify that carefully.
We defined $\alpha_+=\{A\in\alpha:\mu(A)>0\}$ and enumerated it as $\{A_k:k\in J\}$. For each positive-measure atom $A_k$, the information value on that atom is the finite number
\begin{align*}
c_k=-\log\mu(A_k).
\end{align*}
This is finite and nonnegative because $0<\mu(A_k)\leq 1$.
Now define
\begin{align*}
N_\alpha = X \setminus \bigcup_{k \in J} A_k.
\end{align*}
This set is precisely the union of the atoms of $\alpha$ whose measure is $0$. Since the partition is countable and its atoms are pairwise disjoint, the countable additivity axiom for the measure $\mu$ gives $\mu(N_\alpha)=0$. Thus changing a nonnegative measurable function on $N_\alpha$ does not change its Lebesgue integral; below we verify this directly for the two functions at hand.
For $x \in X\setminus N_\alpha$, the point $x$ belongs to exactly one positive-measure atom $A_k$. Therefore
\begin{align*}
I_\mu(\alpha)(x)= -\log \mu(A_k)=c_k.
\end{align*}
The indicator expansion
\begin{align*}
S(x)=\sum_{k \in J} c_k\mathbb{1}_{A_k}(x)
\end{align*}
has exactly the same value: all indicator terms vanish except the single term corresponding to the atom containing $x$. The set $N_\alpha$ is measurable because it is the complement of the measurable set $\bigcup_{k\in J}A_k$. On $N_\alpha$, the atom containing $x$ has measure $0$, so the convention $-\log 0=+\infty$ gives $I_\mu(\alpha)(x)=+\infty$. Thus $I_\mu(\alpha)$ is measurable: it agrees with the measurable function $S$ on the measurable set $X\setminus N_\alpha$ and equals the constant value $+\infty$ on the measurable set $N_\alpha$.
Hence $I_\mu(\alpha)=S$ outside the null set $N_\alpha$. We verify the integral equality from the definition of the nonnegative integral. First, $S\leq I_\mu(\alpha)$ pointwise, because the two functions agree on $X\setminus N_\alpha$ and $S=0\leq +\infty=I_\mu(\alpha)$ on $N_\alpha$. Monotonicity gives
\begin{align*}
\int_X S(x)\,d\mu(x)\leq\int_X I_\mu(\alpha)(x)\,d\mu(x).
\end{align*}
For the reverse inequality, take any nonnegative simple function $\varphi:X\to[0,\infty)$ satisfying $\varphi\leq I_\mu(\alpha)$. Remove its values on the null set by defining $\psi:X\to[0,\infty)$ by $\psi(x)=\varphi(x)\mathbb{1}_{X\setminus N_\alpha}(x)$. On $X\setminus N_\alpha$ we have $I_\mu(\alpha)=S$, so $\psi\leq S$ there; on $N_\alpha$ we have $\psi=0\leq S$. Thus $\psi\leq S$ on all of $X$. Since $\mu(N_\alpha)=0$, deleting the values of a simple function on $N_\alpha$ does not change its simple-function integral, so
\begin{align*}
\int_X \varphi(x)\,d\mu(x)=\int_X \psi(x)\,d\mu(x)\leq\int_X S(x)\,d\mu(x).
\end{align*}
Taking the supremum over all nonnegative simple functions $\varphi\leq I_\mu(\alpha)$ gives
\begin{align*}
\int_X I_\mu(\alpha)(x)\,d\mu(x)\leq\int_X S(x)\,d\mu(x).
\end{align*}
Combining the two inequalities yields
\begin{align*}
\int_X I_\mu(\alpha)(x)\,d\mu(x)=\int_X S(x)\,d\mu(x).
\end{align*}[/guided]