The program does not have a feature that will allow you to delete a single company. It is recommended that you instead create a new company and avoid working with the problem company. If that is not an option, you can perform a clean installation of the program. If you do this though, you will lose all Bookkeeper information and have to start over. So, if you already have multiple companies, you will lose all companies' information, not just the problem company. Directions on how to perform a clean install can be found in this article:

How can I completely remove and reinstall Bookkeeper? (KB010064)