Unfortunately, once you have purchased a movie and added it to your library, there is no way to delete it and repurchase a different version of the movie (e.g. a 3D version in your case).
One workaround you could try is to contact Apple Support and explain your situation. They may be able to provide you with a credit or a solution to help you purchase the 3D version of the movie at an additional cost. It's worth reaching out to see if they can assist you with this issue.
Additionally, you could also check if there are any external streaming or rental services that offer the 3D version of the movie that you are looking for. This could be another way to access the 3D version of the movie without having to repurchase it through Apple.