When she leaned against him, John wrapped his arms around her, holding her close. He had never been able to stand to see her cry or have her upset, and his priority even now was finding a way to lessen it. So he held her as she cried, because he knew the weight of this was terrible, and tried to comfort as best he could with whispered reassurances.
"Shh, it's gonna be alright," he murmured. Somehow, it would be. The road Sam seemed headed further down now, John didn't know what lay in store along the way, but he wasn't going to let their son be lost. While killing Sam had been the last resort suggest to Dean the day John had gone to Hell, last resort was what it was, and he intended to make sure it didn't come to that now.