Let $A = \{ \pm e_k \}$, and suppose $Q$ is a rotation that satisfies $QC \subset C$. Then we will show that $QA = A$, which will restrict the possibilities for $Q$.
Since $Q$ is a rotation, we have $\|Qx\|= \|x\|$, and so $Q \partial B(0,1) = \partial B(0,1)$. A rotation is invertible and the inverse is also a rotation, so we
have $Q B(0,r) = B(0,r)$ for all $r >0$.
We must have $QC = C$. There are various ways of seeing this. Suppose the containment is strict, then $C$ contains some open ball that does not
intersect $QC$, which means that the volumes satisfy $m(QC) < m(C)$, which
contradicts $Q$ being a rotation. We also have $Q(\lambda C) = \lambda C$ for
all $\lambda$ (where $\lambda C = \{ \lambda c \}_{c \in C}$).
We also have $C^\circ = \cup_n (1-{1 \over n}) C$, and so it follows that
$Q C^\circ = C^\circ$.
Since $C$ is given by the disjoint union $C = \partial C \cup C^\circ$,
we have $Q \partial C = \partial C$.
Note that $A=\partial C \cap \partial B(0,1)$,
combining the above shows that $QA = A$.
Now count the possibilities for $Q$:
Since $e_1,e_2,e_3$ form a basis, we need only consider the action of $Q$ on these vectors. $Qe_1$ can have $|A| = 6$ values, $Q e_2$ can have $|A|-2 = 4$ values (since $Q$ is injective).
Finally, since $Q$ is injective there are two remaining possibilities. If $Q$ is proper, then only one possibility remains for which $\det Q = 1$.
Hence there are 48 possible rotations of which only 24 are proper.
Aside: I was curious to know if $Q$ is a rotation and $C$ is such that $QC \subset C$ would imply $QC=C$ in general. The answer is negative, for example, let $Q$ be a rotation by 1 radian, and let $C = \{Q^n (1,0)^T \}_{n=0}^\infty$. Since $\pi$ is irrational, all of these points are distinct
and $QC = \{Q^n (1,0)^T \}_{n=1}^\infty \neq C$.