There's a leap you're making I cannot follow.
I agree with this: the physical configuration of neurons, their firings, the atoms that make them, etc, cannot be "right" or "wrong". This wouldn't make sense in reality; it either is or isn't, and "right" or "wrong" are human values. The universe is neither right nor wrong, it just is.
What about the thoughts those neuron firings mean to us? Well, a good argument can be made that they are also not "right" or "wrong" in isolation, they are just phenomena. Trivially, a thought of "2+2=4" is neither right nor wrong, it's only other thoughts that consider it "right" or "wrong" (often with additional context). So the values themselves can be a physical manifestation.
So it seems to me your problem can be resolved like this: in response to a physical configuration we call a "thought", other "thoughts" can be formed in physical configurations we call "right" or "wrong".
The qualities of "right" or "wrong" only exist as physical configurations in the minds of humans.
And voila! There's no incompatibility between the physical world and thoughts, emotions, "right" or "wrong".