Don't be naive. They can hair split the Pardon to death, and prosecute for things that are technically not covered by it.
If they don't prosecute her for abuse of office, they can prosecute her for misusing government resources. Losing paper clips. It does not matter. They will make the crime fit the limits of the pardon because there is so much leeway in the law, they can make criminals out of people when they want to.
Lois Lerner needs to be prosecuted, and like Al Capone, if you can't get someone for murder, extortion and illegal manufacturing and distribution, you can get them for tax evasion.
It does not matter much on what charge Lois Lerner gets sent to prison. It is simply necessary that Lois Lerner go to prison to serve as an example of what happens to a government official abusing their office with the connivance of their superiors.
As "Remo Williams" said of the 11th commandment.
"Thou shalt not get away with it."
You’re imagining a world where that’s going to happen and you’re calling me “naive”?! LOL! Who are you imagining is going to pursue that route in this government? The tooth fairy? The FBI? Maybe Craig Livingstone or Ken Starr!