Instead of hiding out at the old church on the mountain as Dally suggested, Ponyboy and Johnny should have returned to Ponyboy's house and informed Darry of the situation.  Level-headed Darry would have helped the boys come up with a viable solution, which more than likely would have been to turn themselves into the police. 

Ponyboy's abrupt departure genuinely worried his two brothers, and he most definitely should have kept them more informed of his current dire situation.  Both Darry and Sodapop would want to help their brother as well as Johnny reach a reasonable response to Bob's murder.