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).
