"Unfortunate"?
Put yourself in his position. If you have done nothing wrong, but acted to protect your family from an apparent home invasion, and suddenly found yourself not only arrested for attempted murder but also suspended from your work and deprived of your income, would you not consider that to be punishment?
IF he's done nothing wrong. I don't think we know, yet, whether he did anything wrong.
I can't say whether his suspension is right or wrong, or even normal. I don't know about that. But I don't automatically say it's punishment, because we don't know that, either. When you call it punishment, you imply certain things about his bosses' motivations - things you don't know enough about to say for certain. You're saying that they sat in judgment of him, and decided he must suffer certain consequences for his wrong-doing. In reality, it could have just been done for practical reasons (or what they thought were practical reasons), without assuming his guilt, and without personal animus. That doesn't make it a good policy, but that would remove it from the realm of punishment.
Look at it this way. You could claim that Zimmerman "punished" Martin for his criminal behavior. After all, he didn't just lose his job, he was killed. But if you say that, you're saying that Zimmerman sat in judgment of Martin, and chose to mete out punishment. You've changed him from a guy who used lethal force when he had no other good options, to a vigilante.
Frankly, I think throwing around the word punishment like that is childish, whiny leftism.