I came up with a proof that uses less terminology but that may be different from what you brought up in your post [my eyes still glaze over at the words 'congruence class', I am sorry!]
Proof #1: Let $k$ be the smallest positive integer s.t. $q^k \equiv 1 \pmod n$, or equivalently, $n$ divides $q^k-1$. Let $f$ be an irreducible polynomial that divides $X^n-1$ in
$\mathbb{F}_q[X]$ an let $\alpha$ be a root of $f$. Then the equation $\alpha^n =
1$ holds, and as $n$ divides $q^k-1$ it follows that $\alpha^{q^k-1} = 1$ and
$\alpha^{q^k} = \alpha$. Now, let $d$ be the smallest positive integer such that the equation
$\alpha^{q^d}=\alpha$ holds.
Then check that $\alpha = \alpha^{q^d} = (\alpha^{q^d})^2=(\alpha^{q^d})^3 = \cdots = (\alpha^{q^d})^{\ell} = \cdots$,
and thus in particular $\alpha^{q^{\ell d}} = \alpha$ for all positive
integers $\ell$. And so writing $k = \ell d +r$ [with $r \in \{0,\ldots, d-1\}$] plugging in the equation
$\alpha^{q^k}=\alpha$ yields
$$\alpha = \alpha^{q^k}$$ $$= \alpha^{q^{\ell d+ r}} = \alpha^{q^{\ell d}q^{r}}$$
$$= (\alpha^{q^{\ell d}})^{q^{r}} = \alpha^{q^r}.$$ Given
that $d$ is the smallest positive integer such that
$\alpha^{q^d}=\alpha$ and $\alpha^{q^{r}} = \alpha$ with
$r \in \{0,1,\ldots, d-1\}$, it follows that $r$ must be $0$, and thus
on the one hand, $d$ must divide $k$.
On the other hand, as $\alpha^{q^d}-\alpha = 0$ and $f$ is a
irreducible polynomial in $\mathbb{F}_q[x]$, it follows that $f$ must
divide $X^{q^d}-X$ [because they both share a common root namely
$\alpha$]. However, from an elementary result in finite fields, we
know the following: Let $f$ be an irreducible polynomial in
$\mathbb{F}_q[x]$ that divides $x^{q^d}-x$. Then letting $c$ be the
degree of $f$, the relation $c$ divides $d$ holds. So in particular,
the degree $c$ of the irreducible polynomial $f \in \mathbb{F}_q[x]$
that has $\alpha$ as a root, must divide $d$.
So letting $\alpha$ be a root of $X^n-1$ in $\mathbb{F}_q[X]$, and
letting $d$ be the smallest positive integer s.t. $\alpha^{q^d}-\alpha
= 0$, we have established the following: On the one hand, $d$ must
divide $k$. On the other hand, the degree $c$ of the irreducible
polynomial $f \in \mathbb{F}_q[x]$ that has $\alpha$ as a root,
divides $d$. So $c$ must divide $k$, and the result follows.
ETA: Here is another proof Proof #2, that is along the lines of what was outlined in your OP: Let $\mathbb{F}_{q^k}$ denote the field on $q^k$ elements. Note that $(\mathbb{F}_{q^k})^{\times}$ is a cyclic group on $q^k-1$ elements. As $n|q^k-1$ then it follows that there are exactly $n$ elements $\alpha \in (\mathbb{F}_{q^k})^{\times}$ s.t. $\alpha^n=1$, or equivalently, $X^n-1$ factors completely in $(\mathbb{F}_{q^k})^{\times}$. [Use the fact that a cyclic group $G$ on $N$ elements has exactly $n$ elements $g \in G$ satisfying $g^n = e$ iff $n|N$.] So now then let $f$ be an irreducible polynomial in $\mathbb{F}_q[X]$ that divides $X^n-1$. Then, as $X^n-1$ factors completely in $\mathbb{F}_{q^k}$ there is a element $\alpha \in (\mathbb{F}_{q^k})^{\times}$ s.t. $\alpha$ that satisfies $f(\alpha)=0$. Furthermore, as $f$ is irreducible in $\mathbb{F}_q[X]$ and $\alpha$ is in $\mathbb{F}_{q^k}$, it turns out that $\mathbb{F}_q(\alpha)$ is a subfield of $\mathbb{F}_{q^k}$ of cardinality $q^c$, where $c$ is the degree of $f$. We finish this proof that noting that a field of $q^k$ elements has a subfield of $q^c$ elements iff $c|k$, and so the result follows.