He doesn’t really blame God. That is just a pretense. Blaming God gives him some vague form of release. Because he really blames himself. For everything. Before Serenity Valley he was an openly God-fearing man. After the tragic loss, Malcolm Reynolds became simply afraid.

He joined the Independents with high hopes. Those hopes slowly eroded over the years. What Mal fears most is his own hopeless helplessness. He found that things are out of his control. Perhaps out of everyone's control. He stood in shock during the final battle of the war. It was in that moment that he realized that nothing he did really mattered. He could do nothing to change anything. It wasn’t until later that he realized that the Alliance was not in control either. They were (and still are) a mess just as the Independents were. But he is wrong to think he can't do anything that mattered. He took into his protection two young fugitives. It is unclear to me exactly why he decided to keep them aboard Serenity. But he did. He also added an old man to his crew. An honorary member to be sure, but Mal cared for him nonetheless.

It is because I can see this in him that I left the ship. He was thriving. Become more sure of himself as a person who can change things. I didn’t want to be in his way. And it's not as if I don’t see him. Serenity visits Haven often enough. It is good to see them all again. It is good to see Mal, the Mal who is not despairing, but still pretending to blame God.