Magus runs in battle too, so I don't know if it would work.
Another solution would be to hack the sprite assembly of another, unused PC, like Lucca. This still requires graphic hacking and probably sprite assembly though. In the menu, "she" can have the same portrait as Magus and her Techs can be renamed to Magus' Techs to camouflage the difference (since Lucca and Magus don't have curative Techs, no one will notice).
Each time a battle begins, a small event has to be coded to switch the Prophet with Magus, and vice versa at the end of the battle. The Prophet will gain only 75% of the EXP that Magus will gain, and won't learn Techs or TP, but this may be resolved by copy/pasting one's stats to the other's with Mems after each battles.
Edit: I know > I don't know.