Those interventions led to decades of civil war and millions of migrants to the U.S., whom we are now busy deporting at a record pace.

I agree. Every time the U.S. intervenes in Latin America, we are creating thousands of new refugeess and migrants.  And we have innocent blood on our hands if we fail to condemn this in the strongest terms. There's a great interview with Greg Grandin and Dr. Juan Almendares on Democracy Now.  Grandin points out the relationship between the Honduran military and the U.S. government:

The Honduran military is effectively a subsidiary of the United States government. Honduras, as a whole, if any Latin American country is fully owned by the United States, it’s Honduras. Its economy is wholly based on trade, foreign aid and remittances. So if the US is opposed to this coup going forward, it won’t go forward. Zelaya will return, if the United States—if Obama and Hillary Clinton are sincere in their statements about returning Zelaya to power.

http://www.democracynow.org/2009/6/29/coup_in_honduras_military_ousts_president

Roberto Lovato contrasts the uprising in Iran with what's happening in Honduras, while pointing out that the Obama administration can do a lot more than express its "concern":

"...when viewed from the closer physical (Miami is just 800 miles from Honduras) and historical proximity of the United States, the differences between Iran and Honduras are marked and clear in important ways: the M-16’s pointing at this very moment at the thousands of peaceful protesters are paid for with U.S. tax dollars and still carry a “Made in America” label; the military airplane in which they kidnapped and exiled President Zelaya was purchased with the hundreds of millions of dollars in U.S. military aid the Honduran government has been the benefactor of since the Cold War military build-up that began in 1980’s; the leader of the coup, General Romeo Vasquez, and many other military leaders repressing the populace received “counterinsurgency” training at the Western Hemisphere Institute for Security Cooperation (WHINSEC), formerly known as the infamous “School of the Americas,” responsible for training those who perpetrated the greatest atrocities in the Americas.

The big difference between Iran and Honduras? President Obama and the U.S. can actually do something about a military crackdown that our tax dollars are helping pay for. That Vasquez and other coup leaders were trained at the WHINSEC, which also trained Agusto Pinochet and other military dictators responsible for the deaths, disappearances, tortures of hundreds of thousands in Latin America, sends profound chills throughout a region still trying to overcome decades U.S.-backed militarism.