You should normally be able to make just 1 thumbs up per comment. Now if you switch between comments -> 1 thumb up here, 1 thumb up on the other. Then you can go back to the first comment and thumb up again. The current system only prevents from multiple thumbs up on the same item, but if you start thumbing up other items you can return to the first one... It's not perfect, but it does the job.
If you have some specific requirements, then there is a plugin event that you could hook in and reject the votes based on your logic.