Well, I've to look that issue up again, but the microcanonical ensemble is usually defined as follows.
Let [itex]|n \rangle[/itex] be a complete set of orthonormal energy eigenvectors. Then the microcanonical ensemble is defined by
[tex]\hat{R}=\frac{1}{\omega(E,\Delta E)} \sum_{n, E_n \in (E-\Delta E,E)} |n \rangle \langle n|[/tex]
with
[tex]\omega(E,\Delta E)=\sum_{n,E_n \in (E-\Delta E,E)}.[/tex]
This is the maximum entropy under the constraint that the energy of the system is strictly in an interval [tex](E-\Delta E,E)[/tex].
The entropy is given by the von Neumann expression
[tex]S_{\text{MC}}=-\mathrm{Tr} \; \hat{R} \ln \hat{R}=\ln \omega(E,\Delta E).[/tex]
The definition of the entropy by Dunkel an Hilbert also refers to the von Neuman entropy maximized under the constraint that the energy is strictly below the value [itex]E[/itex], i.e., the Statistical operator is given by
[tex]\hat{R}_{\text{DH}}=\frac{1}{\Omega(E)} \sum_{n, E_n \leq E} |n \rangle \langle n| = \sum_{n} \Theta(E-E_n) |n \rangle \langle n|[/tex]
with
[tex]\Omega(E)=\sum_n \Theta(E-E_n), \quad S_{\text{DH}}=\ln \Omega(E).[/tex]
Then of course, the temperature is strictly positive, if defined by the thermodynamic relation
[tex]\beta=\frac{1}{T} = \frac{\partial S}{\partial E},[/tex]
where all the external parameters (like the volume of a container of a gas) are kept constant when taking the derivative, i.e., for a gas [itex]S=S(E,V)[/itex]. In the thermodynamic limit the usual definition of the of the microcanonical and the Dunkel-Hilbert definition of the thermodynamic quantities coincide asymptotically for large systems.
BTW: I guess you refer to the arXiv version of the paper, which is a bit more detailed than the published version in Nature.
I've just found the following inteteresting reference about this issue, where this is explained in much more detail:
R. B. Griffiths, Microcanonical Ensemble in Quantum Statistical Mechanics, Journal of Mathematical Physics
6, 1447
http://dx.doi.org/10.1063/1.1704681