Pardons are granted after someone has been found guilty. So far, Snowden has only been charged of treason and since he's not coming to the US to stand trial, a pardon is not applicable.
Maybe a new constitution amendment could be created to protect legitimate whistle blowers... since you can't count on politicians/Obama to do the right thing.
Pardons are often granted before someone is found guilty. The most famous pardon in US history, Ford's pardon of Nixon, was before he was formally charged with anything. The blanket pardon of Vietnam draft dodgers also wound up pardoning many people who had not yet been charged. A pardon of Snowden would not be improper procedure.
His accepting the pardon would be an admission that he performed the actions in question, but he admits that anyway.
"Dropping the charges" would be more accurate.