SYG says you don’t have to run. But it only applies when you have that option. When you are on your back being beaten you do not have that option, so SYG does not apply. It is simple self defense. And that is what evidence and witness statements say happened in this case.
SYG does more than give one the right of self defense if you could run away but didn't. It also protects one from civil suits by the family of the perp/victim.
Just because he was having his head smashed on the concrete and couldn't run away, Zimmerman is still protected by the state self defense law, which includes the protections of SYG.