It appears, from what I have read - the articlesposted by Watcher seem to cover the possible realities - that Zelaya was deposed constitutionally, if in a rough and ready manner. The general reaction in Latin America has been knee jerk rejection of any military involvement but who was to carry out the Supreme Court's order to arrest him if not the military? This was hardly similar to the attempted coup against Chavez or Chavez' own coup attempt against constitutional President Carlos Andres Perez in 1992 (exact date?). In neither case had the other institutions of government charged the President with wrongdoing. The closest analogy I can think of is the period that led up to Augusto Pinochet's coup against Salvador Allende in 1972. In that case, the Congress and the courts had turned on Allende but neither had directed his arrest. Pinochet acted alone, in the end. The proof was in what happened next. While the coup itself was popular, the expectation was that the armed forces would return to barracks having done the job - they didn't. In HO, the armed forces were directed to take action by the court which was confirmed by the Congress which named Zelaya's successor according to the constitution. Appropriately, Secretary Clinton has not accepted that this was a military coup and the Adminsitration is acting cautiously.
Personally, I think the WSJ article got it right based on what I currently know, and therefore, we should act more forthrightly to support the Honduran congress and the court. That said, more and different information could change my perception.