I don't think so. The tort of malicious prosecution depends on misuse of the courts, not on the outcome in court. A pardon is a separate event, and does not judge guilt or innocence. A pardon is generally viewed as requiring an admission of guilt and repentance, but any express conditions for pardon are attached by the person doing the pardoning.
That said, if Flynn is pardoned (and there is no reason to do so, he is out of legal jeopardy), the defendants in civil lawsuits by Flynn will argue exactly what was proposed - a pardon is the same as "no foul."
This is as nonsensical as charging him in the first place, but you can bet the argument would have traction in our crooked court system.
An interesting question is whether Sullivan's immunity from suit can be pierced as he wanders so far afield from allowed practice. Flynn is paying for Powell to take the appeal for a writ of mandamus to get Sullivan to stop. Is Sullivan liable for malicious prosecution?
Both prosecutors and judges have "absolute immunity," but the kind a judge has is stronger. "Absolute" isn't really "absolute" in the case of a prosecutor.
Here is a case where a prosecutor was in the line of fire: Freddie Gray vs. Marilyn Mosby.
A couple of esoteric points. The DOJ Motion to drop the case says, expressly, "no crime." There is nothing to pardon there. What Sullivan is yapping about, Criminal Contempt, may be viewed at outside of Trump's pardon power! In criminal contempt, the judge is the prosecutor. POTUS can pardon when HIS branch prosecutes. He can't pardon state crimes. Trump's pardon of Arapio was challenged, and the pardon power was unsuccessfully challenged.
Good info.
Thanks.