If Zimmerman's version of events conflicts with with any eyewitness testimony, as well as any other evidence, such as phone transcripts, etc., then he probably will get charges filed against him.
But if there is insufficient evidence to contradict Zimmerman's statements, he'll get the benefit of the doubt, as jury convictions only accrue when there is NO reasonable doubt.
It would appear that from the actual evidence available at the time, that some legal authorities concluded that no charges were to be filed. If negative evidence develps pursuant to further investigation, I'm sure that will change.
As opposed to a special investigator politically issuing an indictment, I think that the most legitimate way to proceed would be to impanel a grand jury, and let the chips fall where they may.
I don’t necessarily believe Zimmerman did anything illegal, but it was pure stupidity getting out the car and pursuing. It made a bad situation much worse. I agree with your assessment of how this should be handled and its a shame is such a political issue now.