It would be much simpler to just kill off the second Source Hunter at the start and proceed with a lone hero, rather than work it into a mod. I've done this and have gotten my party to be a Level 7 Roderick and a Level 1 Scarlett (who is in ashes 99% of the time).
With that being said, it would be interesting to see if a bonus could be applied to the lone hero to make up for their partner being dead. I can't think of a way to do this at the moment though (beyond just boosting their initial stats).
I'm talking about the other hero not appearing at all. Because everytime you get a stone they ressurect and you have to go kill them again. Which is kind of grizzly.
And (here's the tricky part) the exclamation marks that appear over the head that don't go away...