As far as I can recall, I've never had a compulsive thought that woke me up in the middle of the night, but that doesn't mean it can't happen. Your body is programmed so that it'll snap awake at a perceived threat, and an anxious thought can definitely do that if it scares you badly enough. It's basically your mind and body's way of trying to protect itself.
I don't know the specifics of the thought or what time it was "set" for or if that time has already passed, so it's hard to know what kind of advice to give, but the fact that you recognize it as an intrusive thought and part of the OCD should give you some comfort. I don't know about you, but one of my biggest struggles with the intrusive thoughts is that I feel that, in a way, if I worry over the thought, I've got control of it. But I think that really only serves to feed it. As counterintuitive as it may seem, the best thing you can do for the anxiety is just to accept it. Try not to fight the thought so much as to simply acknowledge it and accept it as part of your anxiety. Just remind yourself that a bad thought is only that - a thought - and it doesn't have any bearing on what will really happen.