From what I understand (which may be mistaken) the problem wasn't that Zelaya was trying to order a referendum to change the constitution to allow for a second term as president; the problem was that he was developing close ties with Hugo Chavez, Raul Castro and Daniel Ortega (potentially) to rig any referendum and then any presidential election, and (because of this) the referendum did not have support of Zelaya's party, Honduras' parlement, attorney general or supreme court and they all asked the army to overthrow him.
To put it another way, it wasn't the prospect of a "Free Vote" on changing the constitution that lead to him being exiled it was the fact that anyone who spoke out against him was being found murdered that made everyone nervous.
