He needs to ask for a legal declaration of innocence, something like this: http://standdown.typepad.com/weblog...-files-suit-for-declaration-of-innocence.html
It's not enough to be found not-guilty in this case.
For the most part, a finding of not guilty is the best you're going to get. The only question the criminal court answers is whether the prosecution met their burden of proof to establish beyond a reasonable doubt that the defendant was guilty of the charged crime.
What you posted is in the case of someone who has been convicted of the crime, and then subsequently released and is now seeking compensation from the state for wrongful incarceration. That's a different case - he wants the court to say that he was released because he was innocent, not because of what is commonly called a 'technicality' (and what lawyers sometimes call 'the Constitution' or 'the law' ).
A case for malicious prosecution will be very difficult to make out here, probably. First, remember that prosecutors and judges generally have absolute immunity for their official actions. Also, anything said in court is absolutely immune from most causes of action. But, let's say that you did want to bring a malicious prosecution claim...
Malicious prosecution requires (speaking generally, different states have different requirements, of course) that the case be brought without probable cause, that it be terminated in favor of the maliciously prosecuted party, and that there be intentional and malicious intent behind bringing the suit (scienter). Here, there almost undoubtedly was probable cause. There was a witness who said that the abuse happened, and the EMT's partner corroborated her testimony. Unless she recants, and says she made it all up, the case isn't going to go far.
Also, remember that litigation, especially criminal litigation, is a very difficult and wrenching matter for most people. It's entirely likely the now-exonerated defendant won't want to go anywhere near a courtroom anytime soon. And even if he did, it seems like a long-shot case. Knowing only what I know here, I would tell him to walk away. There would have to be something more to the story to make me think he had a cause of action.
My opinion and two bucks will get you on the bus, but there you go, for what it's worth.