Most of your question is an excellent formulation of a major philosophical issue: whether minds, if they are merely parts of the general causal order, can possibly have the sort of authorship of their actions that would be required to hold them responsible---how can right and wrong get a foothold if we're just machines? Some say there's no problem here; others are more concerned. Rather than attempt a paltry paragraph on current views about this, let me point you to Timothy O'Connor's article in the Stanford Encyclopedia.

One thing I will say, though, is that it is not clear that the worry would be lessened if it turned out that our minds were immaterial "souls". Souls would have to work somehow or other---a full ("God's-eye") understanding of their workings would presumably involve an inventory of the various states, structures, and processes that souls host, together with the "supernatural laws" that describe how these change over time. These laws might be deterministic or indeterministic, but either way our choices would be revealed as the products of a causal order that is not of our own making. Whether it's a natural or a supernatural causal order makes no difference to what generates the worry--how can an action be mine if it's explained entirely by prior states of affairs and causal laws?