I believe the difference between a hotel & a B&B is a B&B only serves breakfast whereas a hotel will serve breakfast along with dinner. For this case if it was a hotel or B&B is completely irrelevant.
Second positive discrimination is primarily seen in employment. Most common case would be in the area of job application / job promotion. As I understand it, positive discrimination happens if you have two applicants that are equal and the only difference is one of them falls into a protected class (e.g. race, religion, disability, sexual orientation, or age). In that case you can choose the person who falls into the protected category over the applicant and use that reason as your basis for selecting them. However when you look at this story positive discrimination is not applicable.
At least for me, I agree with the judge and feel it is the correct decision. If a judge ruled against the gay couple it would set a dangerous precedent whereby other hoteliers could discriminate against customers on other basis and in the extreme situation it could create chaos when it comes to booking a hotel room since your reservation could be rejected solely on the basis the person did not like you. Also, I believe religion is not defence for all actions and you must be willing to try to get along with all people. In this case, if the owners did not want to have gays staying at their business then they should have found another business that was more in-line with their beliefs.