Thought and emotion are actually separate events. They are often associated together through learning, and therefore can be disassociated through learning too.
Thought arises from the mind.
Emotion arises from the body and is perceived as feeling.
Thought can trigger emotion and likewise the other way.
Intrusive thought disrupts us but doesn’t disturb us as negative emotion does.
So it might be easier to deal first with the emotion that accompany the thought then to deal directly with the thought itself.
Since emotion arises from the body, to ease the emotion you relax the body.