The question is in subject.
I suppose theUpdate: See Andreas Thom's answer to be "yes", because every separable $C^*$-algebra could be represented as a subalgebra of the algebra $B(H)$ of bounded operators on (the) countably generated Hilbert space $H$, and the subalgebras of $B(H)$ should form a set.
Is there any flaw in this reasoning?