The criminal charge has to be disposed of, somehow. I can envision the state's murder charge being ruled invalid, but the state would probably substitute manslaughter for murder II, leaving a criminal charge standing.
Zimmerman's self defense claim can prevail in one of two ways. Either as a finding by a judge, or by a jury. If the finding is by a judge (before, or even after trial), then he will have obtained statutory immunity. If Zimmerman prevails by a jury finding that the state did not disprove self defense, beyond a reasonable doubt, then Zimmerman is subject to a lawsuit for civil liability.
The logic is fairly simple. The standard of proof for a finding of self defense by a judge is the same as the standard of proof in a civil trial. If the court finds it more likely than not that Zimmerman acted in self defense, then the court won;t allow a separate finding in the opposite direction. There is also the legislative intent to spare a person who is justified in protecting himself from the ordeal of trial, and being subjected to money damages for a legally justified act.
There is of course the outcome in the other direction, a jury finds Zimmerman not justified in his use of force. He would face civil liability as well.