Well, it is funny that one of my shortest posts got the most responses. To be clear, I know less about Central America than nearly any other place on the planet. But let me consider the general situation and the application of civil-military concepts.
Yes, President Zelaya sought to act against the will of the Honduran Supreme Court and of the Congress. But, what was the urgency to have the military step in? How was the President funding the referendum? Is there a national police force that could have implemented a court order to arrest the President? What is the process by which Honduras can impeach or remove a President? The CNN reports a process that seems a bit, ahem, dicey.
I am not saying that Zelaya should have been allowed to do whatever he wanted, but I am asking how would a process work, according to the Honduran Constitution. This outcome might be the best for Honduras, but the process by which it came about may be very problematic.
Let me suggest another example: I believe it was the August coup in 1991 in the Soviet Union (but it might have been another event in Russia in the early 1990s). During this coup, the commander of the Strategic Rocket forces issued an order to have all of the mobile missiles return to base so that control is not lost during the disorder. Do we find this decision reassuring? Well, somewhat, as this commander did not have the authority to make this decision. So, we get the right decision, but only because we (the world) was lucky that the right guy was in the right spot.
In Honduras, the military now seems to have the role of deciding when the President is acting in accordance with the Constitution. Is this a good thing for long term democratic stability? I am not so sure.
For the American example raised in the comments, the more apt parallel is not that the military should have exiled GW Bush for the absence of WMD in Iraq, but the contested 2000 election. At no time did anyone seek to ask the military's opinion on whether Bush or Gore won the election. I was not pleased with the Supreme Court's decision, and we are still paying the price. But I would prefer a bad Supreme Court decision to the intervention of the military. It is the job of Congress to remove the President via an institutionalized process, one that is quite difficult to achieve.
Militaries often claim that they are acting on behalf of the public against corrupt leaders, and many times they are. But they often do not return to the barracks.
I am a big believer in process. It sometimes leads to bad outcomes, but the classic question in civil-military relations is: how guards the guardians? If the military sees itself as having a role in the political system, who stops it when it is wrong.