No, the killings are not the same.
Yes, they are going too far.
The killer of Trayvon Martin is a well established non-racist.
The killer is, on the other hand, an idiot about what his role was: a part of a neighborhood watch.
The killer should have left any questioning to the police, and he should not have taken the law into his own hands.
What I find racist about the incident is the way the police handled the incident. The police only needs probable cause to make an arrest, and the body of an unarmed teenager is pretty good probable cause.
As to whether the killer was reasonable suspicious. I don't know how Trayvon was dressed (so I can't speak definitively), but I have seen how teenage black young men often dress in an almost slum like manner. How would you react if ANYONE dressed like that walked into a gated community?
The killer reacted the wrong way. The police told him to back off and he didn't. Now an innocent boy is dead. The killer will be forever scarred by this, and his name will live in infamy long after he dies. Such a waste, such a waste.