"Stay Golden" means that johnny wants ponyboy do to good in life. To achieve his goals in life. Also to do the right choices and to stay out of trouble.
What Dally means when he says "...Crazy for wanting Johnny to stay outs trouble, for not wantin' him to get hard. If he'd never have to run into that church. Thats what you get for helpin' people. Editorials in the paper and a lot of trouble... You'd better wise yourself and nothin' can touch you..." means that he wanted Johnny and pony to not go in that church because, he knew that something was going to happen to them. And know he wants pony only to worry about his self and no one else and he wont get hurt like Johnny did.