do you think that jhonny was justified in killing bob?

Sure he was. Bob was drowning Ponyboy in a fountain. Johnny didn't know if Pony was dead or alive. Johnny was not big enough to knock a guy like Bob out so, in his panic, he did what he had to do.

Johnny had tworked choices..either to let his best friend die and feel guilty for it, or kill someone that would save his best friend. You choose what you would have done but Johnny did the right thing.