They were not acquitted of possessing firearms in a federal facility- they were acquitted of conspiracy to impede federal employees from doing their jobs. 
"But jurors rejected that argument. And under the instructions given to them by Judge Brown, if there was no conspiracy, they could not find the defendants guilty of firearms charges. "
http://www.seattletimes.com/seattle-news/crime/verdict-near-in-malheur-wildlife-refuge-standoff-trial/
Prosecutors chose the biggest charge they thought they could level against these yahoos . Conspiracy is hard to prove and proving these folks did anything like plan anything would seem to be a lost cause to me.
 Wish they had been prosecuted for costs of damage to federal property and made to pay. Likely would have flown.