I think our best course would have been to stay clear.
Staying "clear" is very close to essentially agreeing with the coup. It wouldn't have been as blatant as Bush's tacit endorsement of the coup against Chavez, but in the face of a universal condemnation from the OAS, the EU, and pretty much every responding country and organization in the world, it would be a clear signal that we approved of the coup, or at least its results.

Moreover, that members of the coup itself have doubts about its "legality" can be seen in the faked resignation letter and the immediate declaration of martial law, as well as the clampdown on opposition media.

As for "jumping in to his eyeballs", needless to say I disagree. The Administration didn't recall the Ambassador, didn't declare an immediate cutoff of its quite significant military aid to Honduras, didn't call for Zelaya's immediate reinstatement, etc. The Administration did the minimum required to stay in step with the rest of the world.