TL;DR: Go to Majorana representation, and then it's a bunch of linear algebra.
This turned out a lot lengthier then I expected. I'm sure that there is some clever group-theoretic one-line proof, but here I also provide a construction of the isomorphism, which I think might be useful. I believe there is a lot that can be improved, so I'm open to all comments and suggestions!
Lemma: $N(S)$ is equal to the centralizer $C(S)$.
Proof: Let $h$ be an element of $N(S)$. By definition $N(S) = \{h\in\mathcal{G}_n\;|\;\forall s\in S: hsh^{-1} \in S\}$. For any $g,g'\in\mathcal{G}_n$, we have $gg' = \pm g'g$. Then, we know that
$h g_i h^{-1} = \pm g_i \in S$, However, $-1\notin S$, so it must be that
$h g_i h^{-1} = g_i$. Hence, the normalizer of $S$ is equal to its centralizer $C(S)$.
Majorana representation
Let's use Majorana representation for the Pauli group. We define Majorana operators
\begin{align}
\gamma_1 &= X\otimes I^{\otimes(n-1)} \\
\gamma_2 &= Y\otimes I^{\otimes(n-1)} \\
\gamma_3 &= Z\otimes X \otimes I^{\otimes(n-2)} \\
\gamma_4 &= Z\otimes Y \otimes I^{\otimes(n-2)} \\
&\vdots \\
\gamma_{2n-1} &= Z^{\otimes(n-1)}\otimes X \\
\gamma_{2n} &= Z^{\otimes(n-1)}\otimes Y
\end{align}
In general
\begin{equation}
\gamma_{2i-1} = Z^{\otimes (i-1)}\otimes X \otimes I^{\otimes (n-i)}\,,\qquad
\gamma_{2i} = Z^{\otimes (i-1)}\otimes Y \otimes I^{\otimes (n-i)}\,.
\end{equation}
We have $\gamma_i^2 = 1$ and $\gamma_i\gamma_j = -\gamma_j\gamma_i$ for $i\neq j$. We can also write down an inverse relation
\begin{equation}
Z^{(i)} = \gamma_{2i-1}\gamma_{2i}\,,\qquad
X^{(i)} = \gamma_1\dots \gamma_{2i-1}\,,\qquad
Y^{(i)} = \gamma_1\dots \gamma_{2i}\,,\qquad
\end{equation}
where $P^{(i)} = I^{\otimes(i-1)}\otimes P \otimes I^{\otimes(n-i)}$, $P\in\{I,X,Y,Z\}$ denotes Pauli operator acting on $i$th qubit, and we use convention $XY=Z$.
Any Pauli string can be written a product of Majorana operators:
\begin{equation}
\mathcal{G}_n \ni \alpha g_{\boldsymbol{a}} = \alpha \gamma_1^{a^1}\dots \gamma_{2n}^{a^{2n}}\,,\qquad a^i\in\{0,1\}\,,\qquad \alpha\in\{\pm 1,\pm i\}
\end{equation}
so we can represent any Pauli string using a vector $\boldsymbol{a} = (a^1,\dots, a^{2n})^T$ and the global phase $\alpha$. Multiplication of two Pauli strings $\boldsymbol{a}$ and $\boldsymbol{b}$ is equivalent to addition of their vectors $\boldsymbol{a} + \boldsymbol{b}$ modulo 2. We will thus treat $\boldsymbol{a}$ as elements of a vector space over a $\mathbb{Z}_2$ field. Then, the set of generators $g_i$ is independent iff their corresponding vectors $\boldsymbol{a}_i$ are linearly independent (again, modulo 2).
A product of two Majorana strings is
\begin{equation}
g_{\boldsymbol{a}} g_{\boldsymbol{b}}
=
(-1)^{b^1(a^2+\dots+a^{2n}) + b^2(a^1 + a^3+\dots+a^{2n})+ \dots}
g_{\boldsymbol{b}} g_{\boldsymbol{a}} \,.
\end{equation}
$g_{\boldsymbol{a}}$,$g_{\boldsymbol{b}}$ thus commute iff
\begin{equation}
\boldsymbol{a}^T Q \boldsymbol{b} = 0\,,\qquad
Q = \begin{pmatrix}
0 & 1 & 1 & \dots \\
1 & 0 & 1 & \dots \\
1 & 1 & 0 & \dots \\
\vdots &\vdots &\vdots &\ddots
\end{pmatrix}\,.
\end{equation}
Matrix $Q$ is invertible ($Q^2 = 1$).
Finding the centralizer
We introduce an $(n-k)\times 2n$ matrix
\begin{equation}
A =
\begin{pmatrix}
\boldsymbol{a}_1^T \\
\vdots \\
\boldsymbol{a}_{n-k}^T
\end{pmatrix}
=
\begin{pmatrix}
a_1^1 & a_1^2 & \dots & a_1^{2n} \\
\vdots & \vdots & \ddots & \vdots \\
a_{n-k}^1 & a_{n-k}^2 & \dots & a_{n-k}^{2n} \\
\end{pmatrix}\,,
\end{equation}
whose rows are linearly independent (because $g_i$ are independent). The nullspace of this matrix is $(2n-(n-k))=(n+k)$-dimensional. The condition for Pauli string $\boldsymbol{b}$ to commute with all $\boldsymbol{a}_i$ (i.e. to be in the centralizer $C(S)$) is
\begin{equation}
AQ \boldsymbol{b} = 0\,.
\end{equation}
Since $Q$ is invertible, the dimension of nullspace of $AQ$ (which is the dimension of $C(S)$), is same as $A$, which is $(n+k)$. $S$ is $(n-k)$-dimensional, thus $C(S)/S$ has $\dim C(S) - \dim(S) = 2k$ independent generators.
Isomorphism
Now we will construct the isomorphism with $\mathcal{G}_k$.
We proceed as follows:
Take from the nullspace of $AQ$ an element $\boldsymbol{z}_1$ linearly independent of $\boldsymbol{a}_i$s, and let
\begin{equation}
A_1 =
\begin{pmatrix}
\boldsymbol{a}_1^T \\
\vdots \\
\boldsymbol{a}_{n-k}^T \\
\boldsymbol{z}_1^T
\end{pmatrix}\,.
\end{equation}
We find the nullspace of $A_1 Q$ (which is $(n+k-1)$-dimensional), and take from it an element $\boldsymbol{z}_2$ linearly independent of $\boldsymbol{z}_1$ and $\boldsymbol{a}_i$. Now let
\begin{equation}
A_2 =
\begin{pmatrix}
\boldsymbol{a}_1^T \\
\vdots \\
\boldsymbol{a}_{n-k}^T \\
\boldsymbol{z}_1^T \\
\boldsymbol{z}_2^T
\end{pmatrix}\,.
\end{equation}
and repeat until you get $\boldsymbol{z}_1,\dots, \boldsymbol{z}_k$. At this point $A_k$ will be a $n\times 2n$ matrix, thus the nullspace of $A_kQ$ ($n$-dimensional) will not have any elements liearly independent of $\boldsymbol{z}_j$ and $\boldsymbol{a}_i$.
We use $\boldsymbol z_i$ to construct operators $\tilde Z_i = g_{\boldsymbol{z}_i}$. By construction $\tilde Z_i$ all pairwise commute, and commute with all $g_i$. They will be $Z$ operators of $\mathcal{G}_k$. To find the $X$ operators, we must find $\tilde X_i$ such that,
- $\tilde X_i \tilde Z_i = -\tilde Z_i \tilde X_i$ and
- $\tilde X_i \tilde Z_j = \tilde Z_j \tilde X_i$ for $i\neq j$ and
- $\tilde X_i g_j = g_j \tilde X_i$ and
- $\tilde X_i \tilde X_j = \tilde X_j \tilde X_i$
We proceed similar as before. We find $\boldsymbol x_i$ ($i=1,\dots k$) by solving
\begin{equation}
A_k Q \boldsymbol x_i = (\underbrace{0,\dots, 0}_{n-k+i-1},1,0\dots)^T \equiv \boldsymbol e_{n-k+i}\,,
\end{equation}
where $1$ on the right hand sides accounts for anticommutation condition 1. $\boldsymbol x_i$s are only defined up to the nullspace of $A_kQ$. This will be necessary to satisfy condition 4.
The generators of nullspace of $A_k Q$ are the rows of $A_k$. Thus for our solutions $\boldsymbol x_i$, which satisfy condition 1-3, we can take
\begin{equation}
\boldsymbol x'_i = \boldsymbol x_i + A_k^T \boldsymbol r_i\,,
\end{equation}
which also satisfy these conditions. Now we want to make sure that $\tilde X_i \equiv g_{\boldsymbol x'_i}$ commute with each other (condition 4). This is equivalent to
\begin{equation}
\boldsymbol x'^T_j Q\boldsymbol x'_i = 0 \\
(\boldsymbol x_j^T + \boldsymbol r_j A_k) Q (\boldsymbol x_i + A_k^T \boldsymbol r_i) = 0 \\
\boldsymbol x_j^T Q \boldsymbol x_i + \boldsymbol x_j^T Q A_k^T \boldsymbol r_i +
\boldsymbol r_j^T A_k Q \boldsymbol x_i = 0 \\
\boldsymbol x_j^T Q \boldsymbol x_i
+ \boldsymbol e_{n-k+j}^T \boldsymbol r_i +
\boldsymbol r_j^T \boldsymbol e_{n-k+i}
= 0 \\
\boldsymbol x_j^T Q \boldsymbol x_i
+ r_{i,n-k+j} +
r_{j,n-k+i}
= 0\,.
\end{equation}
$i,j=1,\dots k$, and each pair $i<j$ corresponds an independent equation. This gives $k(k-1)/2$ independent equations. $r_{i,1},\dots,r_{i,n-k}$ are arbitrary, since they correspond to multiplying $\tilde X_i$ by one of the stabilizers $g_i$. This leaves $r_{i,n-k+1},\dots,r_{i,n}$, $i=1\dots k$, as variables, of which there are $k\times k$. Thus the (relevant) solution space is $k(k+1)/2$ dimensional.
We can check our counting for a simple example $n=k=2$. $k(k+1)/2=3$, so there should be $2^3=8$ independent solutions. Let $\tilde Z_1 = Z\otimes I$, $\tilde Z_2 = I\otimes Z$. The possible choices for $\tilde X_1$, $\tilde X_2$ are then $\tilde X_1 = P_1 \otimes P_2$, $\tilde X_2 = P_2\otimes P_3$, where $P_1,P_3 \in \{X,Y\}$ and $P_2 \in \{1,Z\}$.