This is a really tricky question.

On his side, I've seen questions similar to yours when the couple could never stop, where the relationship doesn't end. But then again, there are questions when they do end it entirely and at least one of the couple, let's say your boyfriend, spends the rest of his life feeling guilty about it.
Before we transition to your side, I do need to point out that this was a secret he had been harboring and something he does feel guilty about...but he told you. So he trusts you enough to tell something he has never told anyone and trusts you will never tell.

Now, your side. It's normal to feel confused, but you did pressure him into telling you something he wasn't comfortable enough to tell anyone. So here is what you have to decide: Can you live with this information? Can you live with breaking up with him because of something you had forced him to tell you? Are you going to be holding this over his head during family dinners or arguments with him? Would you tell someone or are you sworn to secrecy?

Personally, if I was in your position, I'd be just as confused. I would be doing the same thing you are doing and be asking what the best move should be. But the questions above are questions I would be asking: can I live with someone who had a romantic relationship with a relative, would this relationship continue, and would I want to still be in this relationship? Only you can answer that.