Ouch! You really are in a pickle - but there is a solution.
The first thing to consider is the length of time this mentor/mentee relationship is suppose to last. Is it for the rest of the school year or just another month? If it's a shorter amount of time, I would just let it run it's course and correct the distribution for next year. Once the damage has been done, it is very difficult to reverse.
However, if this is something you must fix now - just dive into it and simply tell the students the truth - that them picking mentors has created an imbalance system that is not beneficial to them.
You need to state it this imbalance is hurting them and that the program re-organization will give them the best chance for success. You need to stress how it is for their benefit.
Then just do it, match them up as best as possible and get to it. You can not please everybody in this situation but you can make a change for the greater good. If some one really has a problem, you can look into it but they are young kids, you have to show them what is best.