Well I guess by "honest rape" he meant that the person has actually been raped compared to someone merely lying that she has been raped in order to get an abortion.
Yeah, that is evident from the context. But the phrase itself is ridiculous.
You know what my problem is, honestly? It was a stupid fight to pick. He could have just said, "I believe there should be an exception for rape" & left it at that. That you have to have really been raped is sort of implied. If he didn't, then when asked how he'd determine if a rape was honest, he could have said, "Courts have a system for this, it's already taken care of." Instead, he stumbled around looking for an answer before finally admitting that he'd have to take it on faith.
So all he did was make himself look like a stupid, paranoid, indecisive asshole who has no idea how the government works. Exactly the kind of person who should be President. And it all could have been avoided. In so many ways.