"Does God judge us by our thoughts?"

In Orthodox thinking, yes. But, the thoughts are no more of a sin than any other, besides refusing the urging of the Holy Spirit. The only distinction between sins is whether they're legal or not. You can't be arrested for thinking, but you can be arrested for doing something about your thoughts.

In both cases, the sin is that the act, whether physical or mental, distracts us from the Holy Trinity.