Yes, there is a difference.
If you think something over, you are considering it's good point and it's bad points, what is likely to work, etc. You may be making a decision about whether or not to do something.
If you think something through, you MAY do the same things, but you are picturing the situation at its logical end. You may be trying to solve the problem or figure out the final consequent.
If I ask you to go to lunch at a Thai restaurant and you don't know if you like Thai, you may think that over to decide if you're brave enough to try something new. However, if I ask you to go to lunch somewhere with a lot of greasy food and you are trying to loose weight, when you think it through, you may decide it's not a good idea to go.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.