This article has a interpretation vey different from other one´s I have read (dont have the links now) and heard (I am a law student, and almost all the International law teachers here were against that).
Just to point on thing, using the article you sent:
"On June 26, the Chief Prosecutor filed a Criminal Complaint before the Supreme Court
of Justice, requesting that Zelaya be arrested under an accusation of the crimes of acting against the established form of government, treason against the country, abuse of authority, and usurpation of functions. On the same day, the Supreme Court of Justice unanimously voted to appoint one of its Justices to hear the process in its preparatory and intermediate phases; that Justice carried out the request, issuing an arrest and raid warrant. Two days later, on June 28, 2009, Zelaya was arrested."
You can´t have the due process of law in a decision made in one day and with no opportunity for the defense.
Also the justification used from the Honduras court (and same on this paper) was that the "Constitution grants the courts the authority to apply laws to specific cases and to adjudicate and enforce judgments", but you apply the law that way, the Supreme court can´t do whatewer they want, which is not true in any legal state.