You are right, evil thoughts are not automatic, but this does not prove in the slightest, that someone is incapable of evil thoughts.
To be able to judge wether an action is evil before it is done, I must have knowledge of what the result of said action would be. To know that, I need to know that my actions influence others. And to know that I need to be able to think about my actions, or the actions of others. Only then can I form a judgement wether an action is good or evil. Since inherently, no action is good or evil. If something is done, it simply "happened". It is only through us judging that action that we can say that it was good or evil or neither.
The same could be said for God. Maybe he thinks about doing something hurtful to a person, to set said person on the right path. Wether he actually would do it, I don't know.