This paper proves that there is no functor from the category of C* algebra (and morphisms) to the category of locales/topological spaces/a lot of other things that extend the gelfand duality and send matrix algebra for $n >2$ to some non-empty space. Composing your eventual "center functor" with gelfand spectrum would give such a functor.
PS : It is not completely clear from the statement in paper, but they do ask that the functor extend the Gelfand duality on object AND morphisms. So you might hope to obtain such a functor in a way that don't let the morphism of commutative algebra act naturally on the center... But this seems also impossible: if you look at the proof in the paper you only need your functor to be the natural thing on $\mathbb{C}$, $\mathbb{C}^2$ and $\mathbb{C}^3$ are morphisms between them to obtain that the image of $M_3(\mathbb{C})$ is degenerate, and because any functor have to preserve spliting of projection I would bet that no assumptions on morphism is required.