On the one hand, the Pope has called for dialogue to "ensure peaceful coexistence and authentic democratic life" in Honduras.
On the other, Tracy Wilkinson at the L.A. Times published an article questioning the role of Cardinal Oscar Andres Rodríguez Maradiaga in the coup as well as its aftermath:
Nine days after the coup and two days after Zelaya attempted unsuccessfully to land at the airport, the cardinal was overheard on his cellphone to the attorney general, urging him to produce drug trafficking evidence against Zelaya. "My son," he said, "we need that proof. It's the only thing that will help us now."
I've mentioned the Cardinal's role before, and comments suggested there may be a split between the Church hierarchy and local parishes. There are still a lot of untold stories.