Comey’s speech was very clear about the results of his investigation. He explained how Clinton’s conduct was not anything that would normally be prosecuted.
But that’s not the same thing as ‘not committed a crime.’
Here is an analogy: you are walking along your favorite hiking trail and you see a magnificent sight. A bald eagle swoops down and kills a young raccoon caught in the open. (Well, grisly and magnificent all at once, perhaps). As the bird flies away with its prize, you see a single feather left behind on the ground and decide to keep it, at least long enough to validate your story as you tell your friends.
This is not the kind of conduct that would normally be prosecutable. I doubt the federal government would ever choose to ask a grand jury to indict you for those facts.
But it’s a crime: as everyone should remember, 16 U.S.C. § 668(a) provides that anyone who knowingly transports or possesses any part of a American bald eagle shall be fined not more than $5,000 or imprisoned not more than one year or both. There is an exception for scientific or exhibition purposes of public museums, scientific societies, and zoological parks, or for the religious purposes of Native Americans, but not for your desire to commemorate your sight of the eagle on your hike.
In shorter words: it’s technically a crime, but not a set of facts that would ever be prosecuted.
This is true also with Clinton’s conduct.
18 USC § 793(f) provides anyone who, through gross negligence, transmits classified information to an unauthorized person is subject to fine or imprisonment. Comey’s point was that no one has ever been prosecuted for negligently violating this law – despite a constant barrage of claims like, “If I did that, I’d be in jail!” the truth is that prosecutors have never chosen to bring criminal charges unless the motives for disclosure went beyond negligence and into profit, or emnity/revenge/animus.
We don’t typically prosecute people for picking up the feather, in other words, even though the act is technically a crime. In Clinton’s case, the strict letter of the law is that her acts could certainly serve as the basis for an indictment, and if a jury believed her conduct was grossly negligent, is legally sufficient to sustain a conviction.
It’s just never done, because it’s a hypertechnical application of the law.
That was the substance of Comey’s message, and (in my view) it was essentially correct.
So, now we imagine Trump making the decisions. He’s already signaled that he does not intend to pursue the matter, of course, but Trump is nothing if not mercurial. He could certainly find a slimy but ambitious special prosecutor and say, in effect, “Pretend Clinton plays lacrosse and you’re Mike Nifong. Get her!” And the subsequent prosecution would be unprecedented, but it would certainly rest on probable cause to believe that Clinton committed an actual act that was, at least technically, a crime.
tl;dr – she technically did commit a crime, and it’s possible but unlikely that she would need a pardon because Trump has shown himself vindictive, unethical, and unpredictable.