Here's the way I see it:
This notion that Zelaya was seeking to be re-elected seems dubious. His attempts to amend the Constitution in Congress were rejected so he was organizing a national referendum on whether a Constitutional Assembly should be called to reconsider the one term limit on the executive branch. The question on the poll was roughly:
""Do you agree that, during the general elections of November 2009 there should be a fourth ballot to decide whether to hold a Constitutional Assembly that will approve a new political constitution?"
Thusly, if the poll had a Yes verdict the ballot in question wouldnt even be up for actual approval until the elections in November... you know the ones that Zelaya can't legally run for. Therefore the ballot initiative could not help him gain any power. He would be out of power even if a "Yes" to this Constitutional Assembly came back.
Secondly, this referendum was non-binding and was probably a political attempt to show that there was support for such a measure (longer presidential terms). The backing of the survey, though rejected by the Congress, had been petitioned by I believe over 800,000 honduran citizens (I believe roughly 12-15% of the population).
Thirdly, the Honduran Constitution does not forbid asking a referendum to convene a Constitutional Convention. Article 239 in the Constitution does forbid elected officials from seeking the abolition of term limits. However it is not a criminal act (only the stripping of his powers is called for). I've yet to see (not to say it does not exist but still I've yet to see) any transcript of any speech or communication by Zelaya that has violated this Article and sought the outright abolition of term limits. The Honduran Supreme Court to my knowledge has never RULED that Mr. Zelaya has broken this Article either (and a midnight military coup is hardly a legal ruling).
The Honduran Supreme Court is not given the right to command the military at any juncture (and if I read correctly Article 312 forbids it), which is what it appears they have done here. Barring a criminal offense (of which Zelaya has not actually been accused of) the military does not have the right to exile or imprison any elected official (or person for that matter). Laughably Article 81 FORBIDS exile as a use of punishment since that article guarantees that every citizen has the right to exit and enter the country freely. Article 2 declares that usurping popular sovereignty and supplanting constituted powers are treason against the state. Seem to me that illegally removing the elected Head of State would violate that Article as well.
Even if I have misinterpreted this situation and President Zelaya was in some kind of gross misstep of the law, this does not in any way condone the midnight removal by the military under alleged urging of the Supreme Court of the Head of State and his exile and the subsequent cut of communications in the capital and the crackdown on journalists. This passes all the tests in my book of being a coup. It's also sad that Conservatives are immediately attacking Zelaya because he is allies with Chavez and obviously since Chavez seeks indefinite presidential reign therefore his allies must as well
(Morales agreed he would not seek a way to be reelected for a third time in 2014 btw). I believe the Conservative factions of the Western Hemisphere are getting worried that now every Latin American Nation has a democratically elected leftist ruler (some 16 countries or more) except for I believe Mexico, Argentina, and Colombia.