Thanks guys,
No spare pins I'm afraid, that would be too easy!
It's more or less a development board, so there isn't really any specifications; I was aiming for versatility. I think you're right that the only purpose the isolation would really serve would be to prevent a potential ground loop. It doesn't seem like that's enough benefit to justify the much greater BOM cost. And yes, the box dimensions are fixed, so I can't really add a second header.
Out of curiosity, does anyone know if there are actual recommended isolation levels for, say, an Automotive CAN bus? I'm having trouble finding anything like that.