The government does not run the elections in Honduras. A special committee called the Supreme Electoral Tribunal (TSE in Spanish) is the one that does all that. The TSE is an independent, autonomous institution that has nothing to do with any of the three branches of government. TSE runs the whole election show, not Micheletti, not Zelaya, not the military, not the congress, not the Supreme Court, but the TSE.
If you need proof that the TSE is independent:
In 1981 when Honduras was under military rule, the military and the Nationalist Party ran the three branches of government and the Liberal party won those elections.
In 1989 the Liberal Party controlled the three branches of government and the Nationalist Party won those elections.
In 1993 the Nationalist Party ran the three branches of government and the Liberal Party won those elections.
In 2001 the Liberal Party controlled the three branches of government and the Nationalist Party won those elections
And finally, in 2005 when Mel Zelaya of the Liberal Party won the election, the Nationalist Party controlled the three branches of government.
How could all of this have happened in a third world country that does not respect the law or the constitution, where coups happen all the time, and where people are still stuck in the 1970's? Simple, the TSE is a democratic, autonomous, independent institution (Article 51 of the constitution).
The three magistrates of the TSE and the substitute member are selected by congress and serve a 5-year term. The current magistrates were chosen in May 2009, under Mel Zelaya's administration. Nominees for the TSE cannot be directors of any political party or political candidates. During their tenure, they can not assume any paid position except for teacher. They may not participate directly or indirectly in any political activity in any manner except to exercise their suffrage in the elections. (Article 52 of the constitution.)
The TSE has asked several countries to observe the elections and would like to have thousands of observers. They have also indicated that citizens will be allowed to observe the counting of ballots in the polling places. The magistrates have promised the most open, fair, and transparent elections ever.
International observers could help to verify that for the world.