(I'm going to be a bit informal to be able to go to the point relatively directly, but if you want more details on some specific aspect. I can try to add them)
Toposes are closely related to topological groupoids, in fact, they can be seen as a special type of localic groupoids or localics stack, the "étale-complete localic groupoids". (see the other answer)
So because we know very well how to attach a C* algebra or Von Neuman algebra to a groupoid it is very natural to expect that one can attach C* or Von Neuman algebra to a topos. Maybe not in full generality as topos corresponds to very general topological spaces and C*-algebras are attached to locally compact topological groupoids, but at least for 'nice topos' it should be possible. And also topos corresponds to Groupoid up to morita equivalence only, so the algebra we produce in general is only well defined up to Morita equivalence.
In some sense my work on this topic at the time was an attempt to give a direct description of the C* algebra or Von Neuman algebra one can attach to a topos (without going through groupoids) or to describe some properties of the Von Neuman algebra directly in terme of the topos (for example its modular time evolution).
And in fact it is possible:
To get a von Neuman algebra you should start with a Boolean topos that satisfies some 'measurability' condition, consider an 'internal Hilbert space object' in the topos and look at its algebra of endomorphisms. The construction works better if one assume that the topos $T$ is in addition 'locally separated' and take an Hilbert space of the form $L^2(X)$ for $X$ such that $T/X$ is separated. In this case you get a close connection between what I call measure theory over $T$ and the modular time evolution of the corresponding Von Neuman Algebra. This is essentially what I study in the paper you linked.
For C* algebra things are a bit more complicated, the best construction I could get to is described here.
Now, to go back to your question: can we go the other way and attach a topos to a von Neuman algebra or C algebra ?*
Essentially, no. At least not in a very interesting way if we do not have some additional structures. Of course it is not possible to give a definitive negative answer to this kind of question, so I'll say "probably not".
The problem is better understood in terms of groupoids than in terms of topos: the convolution algebra of a groupoids contains a lot of information on the groupoids, but if you consider it as a mere C*-algebras clearly a lot of information is lost.
For example, let's consider a groupoid $BG$ with only one object $*$ and $Hom(*,*)=G$ a group (Corresponding to the topos $BG$ of sets with a $G$-action). The kind of Von Neuman algebra or C* algebra you will attach to this topos is a Groupe algebra of $G$. Now if $G$ is abelian you will obtain an abelian Von Neuman algebra. But Abelian Von Neuman algebras corresponds to ordinary measurable spaces, so in this case you get two very different types of toposes that corresponds to exactly the same von Neuman algebra (a BG, and a topos of sheaves over a Boolean locale). The isomorphisms between the two Von Neuman algebra you get is induced by a kind of "Fourier transform" whose origin is purely analytic and non-geometric (at least in this picture).
What I read on this type of example is that if you want to construct a topos (or groupoid) out of an algebra you need something more. What this "something more" is can vary a lot, to give two example:
For C*-algebra the notion of Cartan subalgebra sometime allow to reconstruct a groupoids, I don't know the literature on this topic but these slides will give you an idea. I assume a similar theory for Von Neuman algebra might be possible.
One expects there will some connection between module for the algebra that one obtains a some kind of bundle of vector space/hilbert space on the topos. These bundle of vector spaces on the topos generally have a "pointwise tensor product". So one expect the Algebra we obtain to have an additional structure that corresponds to this tensor product, i.e. some sort of "generalized bi-algebra structure". One also expect that this tensor product is enough to recover the geometric object (this is very similar to Tanaka theory). I have a draft that I never finished on this topics if want to see a precise statement.
There are probably other similar story that can be told.
So in some sense I see that C*-algebra/Von Neuman algebra attached to a topos as some kind of invariant, like a homology theory. That reveals a lot of important and sometime hidden informations, but definitely not all the informations.
To finish, I would like to comment on the Bohr topos mentioned in the other answer, as it is is the only such construction present in the literature. I want to emphasize that it does not really answer the question in a satisfying way because the "Bohr topos" is not reall a topos, it is only an ordinary topological space. Indeed, because it is a topos of sheaves on a poset, it actually is a topos of sheaves on a locale, and in fact on a topological space due to a compactness argument, so it will never exhibit any "non-commutative" phenomenon. The construction has been formulated in the language of toposes because many people hope it might be possible to modify the construction to actually produce a topos, and maybe it is, but at the present time what is constructed is really just an ordinary topological space.
