Frankly, the reporting on the incident is terrible, with everyone blatantly leaving out crucial facts. Here is what I managed to gather from reading multiple sources of different leanings.
1) No solid evidence showed that the smuggler was either armed or unarmed at the time.
2) Compean and Ramos both failed to report the incident except mentioning "I had to fire some rounds." Only later after the incident was reported from another source, did they mention firing on what they believed to be an unarmed man.
3) Compean removed shell casings and asked another agent to remove shell casings from the incident.
4) Ramos and Compean had holes in their testimony that conflicted.
All in all, it appears that these men were in fact guilty of obstruction of justice, but not assault. There is not evidence to show beyond a reasonable doubt that they shot an unarmed man. However, removing the shell casings, asking another agent to remove casings, and failing to report the incident shows clear intent of a cover-up. I would suggest these men didn't actually commit a crime until they panicked and decided to tamper with evidence and withhold information.
The 12 years conviction comes from mandatory sentencing guidelines requiring at least 10 years for committing a violent crime with a firearm, something the jury was unaware of. In my opinion, they should simply have been conivcted with obstruction of justice ( as was offered in the plea bargin), and let off on the other charges.
Overall, I will agree with Bush's choice to pardon, as the sentence far outweighs the crimes these men actually committed. Furthermore, since they won't serve in the border patrol again, they will be unable to cause further problems by covering-up evidence. A satisfactory conclusion in my mind.