Another fairly simple proof. The key idea is in "Case 3" below: if a point $x \in S$ is a limit point of the collection of intervals, then a sequence of interval endpoints approaches $x$.
Let's say $I_n = (a_n, b_n)$, always with $a_n < b_n$. Note each endpoint $a_n$ and $b_n$ is an element of $S$: $a_n$ and $b_n$ are obviously not in $I_n$, and if either is an element of another interval $I_k$, this would imply $\overline{I_n} \cap \overline{I_k} = [a_n,b_n] \cap \overline{I_k} \neq \emptyset$, contradicting the initial assumption.
Given a point $x \in S$, we explicitly construct a sequence $(x_n)$ in $S$ converging to $x$. Define set
$$ A := \{a_n : n \in \mathbb{N}, a_n > x\}.$$
Case 1: $A = \emptyset$. Then $(x, \infty) \subset S$. Let $x_n = x + \frac 1 n$.
Case 2: $\inf A > x$. Then $(x, \inf A) \subset S$. Let $x_n = x + \frac 1n (\inf A - x)$.
Case 3: $x \notin A$ and $\inf A = x$. Let $m$ be the smallest index such that $a_m > x$ and define
$$ x_n := \min\left \{a_k : k \leq m+n, a_k > x\right\} .$$
This sequence of numbers in $S$ and larger than $x$ is non-increasing. Since $\inf A = x$, every interval $(x, x+\epsilon)$ contains some $a_k$ and $x_n \leq a_k < x+\epsilon$ for all $n \geq k$, so the sequence converges to $x$.
Case 4: $x \in A$. That is, $x = a_k$ for some $k$.
Then $x$ is not equal to any $b_j$: $b_k>a_k$, and for every other index $j$, $[a_j,b_j] \cap [a_k,b_k] = \emptyset$ implies $x = a_k \neq b_j$.
Consider the sequence of intervals $\tilde{I_n} = (-b_n, -a_n)$. Their closures are disjoint, and $-x$ is not equal to the lower endpoint $-b_n$ of any of the intervals. The corresponding set $\tilde S$ is exactly the negative values of $S$:
$$\tilde S = \left(\bigcup_{n \geq 1} \tilde{I_n} \right)^c = \{ -y : y \in S \} $$
So by one of the three cases above, there is a sequence $(\tilde x_n)_{n\in \mathbb{N}}$ with values in $\tilde S \setminus \{-x\}$ converging to $-x$. Therefore the sequence $(x_n)_{n \in \mathbb{N}} := (-\tilde x_n)_{n \in \mathbb{N}}$ has values in $S \setminus \{x\}$ and converges to $x$.