In a democracy, bad leaders are voted out (and Zelaya was most definitely a lousy leader); not removed extralegally. There was certainly a legitimate separation of powers issue here, and Zelaya seems to have been overstepping his bounds in the sense that only Congress has the power to call referendums, but it should have been brought before a judge.

The irony of all this is that he was quite unpopular and almost certainly would have lost the referendum anyway.