These people went to jail because:
1) It's against (American) federal law to import wildlife taken in violation of the laws of another country;
2) The people in question took substantial measures to hide their smuggling activity;
3) The amount of illegal goods in question here was valued at millions of dollars.
The fact that it was no longer illegal in Honduras doesn't matter, though the reason why is rather esoteric. In criminal matters, liability requires two concurrent elements: 1) an act; 2) a certain state of mind. You have to have both at the same time--one by itself won't do.
E.g. if I'm in the woods hunting and I shoot and kill someone thinking they are a deer, I'm not guilty of murder because while I have engaged in every action required to commit the crime I did not have the requisite state of mind.
Here, they imported wildlife, and they did so with the knowledge/belief that the wild life had been taken in violation of Honduran law. They were mistaken about whether the wild life had actually been taken in violation of Honduran law, but as a general rule mistakes do not change the outcome unless the mistake negates the state of mind. In this case, their mistake did not negate their guilty state of mind. The result seems harsh, but it's just the symmetry of the rule. It's no more conceptually unfair than say holding someone guilty of attempted murder.