There are two ways to look at this.

If you believe, you will understand that God is the final judge in any matter. So yes there are gray-scales, but only God knows every detail and factor which went into the 'sin', and only He will know the 'right' answer to the problem.

We humans can only do our best to try and understand how to apply these commands in our lives.

However the Commandments are not absolute. This is even made clear in the Bible. Thou Shalt not commit murder - that's the command, but is going to war to defend your home the same as committing murder? No it's not.

From the agnostic side, we can nit-pick the Bible to death, finding all sorts of inconsistencies in it, but don't assume that you can do this with every religion. Because one religion is wrong, does not automatically prove that all are wrong.

This would be like saying that because Darwin was a racist - and racism is wrong - therefore everything Darwin said was wrong.

Or, because Darwin was a racist, and Darwin wrote the theory of evolution, therefore everyone who believes in the theory of evolution is a racist.

This type of argument will never serve to reach the truth.