An alien thought is a thought that you very rarely have, a thought that is not natural to your way of thinking. . eg He is a very rude person. 'I should be polite' is an alien thought to him.
It makes sense in Clive's context. A thought that is counter to your personality... It doesn't work for me to mean a rare thought. It may be correct, but I don't think many people are familiar with that usage.