From Wikileaks, here is a July 24, 2009 cable from Ambassador Hugo Llorens in Honduras to Washington with an outline of the developing coup. I think it is a good analysis, looking at both sides and concluding without a doubt that Mel Zelaya's removal was both illegitimate and illegal. (I wonder, though, why it took almost a month to write the report--why not just read my blog?)
No matter what the merits of the case against Zelaya, his forced removal by the military was clearly illegal, and Micheletti's ascendance as "interim president" was totally illegitimate.
This only reinforces what we already knew. The Obama administration believed there was a coup and it was totally illegitimate, but chose not to press the issue too hard and to remain publicly vague about its interpretation of the facts.